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Conserved domains on  [gi|1935598096|ref|NP_001375433|]
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peroxisome biogenesis factor 2 isoform 1 [Rattus norvegicus]

Protein Classification

peroxisome biogenesis factor 2 family protein( domain architecture ID 12057473)

peroxisome biogenesis factor 2 family protein such as peroxisome biogenesis factor 2, which is required for uptake of several proteins into peroxisomes

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Pex2_Pex12 pfam04757
Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of ...
27-224 2.49e-39

Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.


:

Pssm-ID: 398431  Cd Length: 213  Bit Score: 137.13  E-value: 2.49e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1935598096  27 KALEQLVWSQFTQCFHGFKPGLLA-RFEPEVKAFLWLFLWRFTIYSKNATVGQSVLNIQYKNDSSPnpvYQPPSKNQKLL 105
Cdd:pfam04757   2 EELESLLRPQLRYILRLLAGQRFPlNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDG---GRLLSRRRRLL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1935598096 106 YAVCTIGGRWLEERCYDLF--------RNRHLASFGKAK------QCMNFVVGLLKLGELMNFLIFLqKGKFATLTERLL 171
Cdd:pfam04757  79 SLLLLVLLPYLLRKLDSLLprlsandlESRNARDSLKSRlkryllKLYPFLESLYKLLNLHLFLFYL-TGKYYSLSKRLL 157
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1935598096 172 GIHSVFCKPQSM----REVGFEymnrELLWHGFAEFLVFLLPLINIQKLKAKLSSWC 224
Cdd:pfam04757 158 GIRYVRLKPLDIfsneRRVSYE----QLLWNAFSELLGFLLPLLLAVILFLKLLEWW 210
RING-HC_PEX2 cd16526
RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as ...
242-288 1.46e-21

RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as peroxisome biogenesis factor 2, 35 kDa peroxisomal membrane protein, peroxisomal membrane protein 3, peroxisome assembly factor 1 (PAF-1), or RING finger protein 72 (RNF72), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It may be involved in the biogenesis of peroxisomes, as well as in peroxisomal matrix protein import. Mutations in the PEX2 gene are the primary defect in a subset of patients with Zellweger syndrome and related peroxisome biogenesis disorders. Moreover, PEX2 functions as an E3-ubiquitin ligase that mediates the UBC4-dependent polyubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation.


:

Pssm-ID: 438189 [Multi-domain]  Cd Length: 49  Bit Score: 85.51  E-value: 1.46e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1935598096 242 KECALCGEWPT-MPHTIGCEHVFCYYCVKSSFLFDMYFTCPKCGTEVH 288
Cdd:cd16526     2 TECAICGEWPTnNPYSTGCGHVYCYYCIKSNLLADDSFTCPRCGSPVS 49
 
Name Accession Description Interval E-value
Pex2_Pex12 pfam04757
Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of ...
27-224 2.49e-39

Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.


Pssm-ID: 398431  Cd Length: 213  Bit Score: 137.13  E-value: 2.49e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1935598096  27 KALEQLVWSQFTQCFHGFKPGLLA-RFEPEVKAFLWLFLWRFTIYSKNATVGQSVLNIQYKNDSSPnpvYQPPSKNQKLL 105
Cdd:pfam04757   2 EELESLLRPQLRYILRLLAGQRFPlNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDG---GRLLSRRRRLL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1935598096 106 YAVCTIGGRWLEERCYDLF--------RNRHLASFGKAK------QCMNFVVGLLKLGELMNFLIFLqKGKFATLTERLL 171
Cdd:pfam04757  79 SLLLLVLLPYLLRKLDSLLprlsandlESRNARDSLKSRlkryllKLYPFLESLYKLLNLHLFLFYL-TGKYYSLSKRLL 157
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1935598096 172 GIHSVFCKPQSM----REVGFEymnrELLWHGFAEFLVFLLPLINIQKLKAKLSSWC 224
Cdd:pfam04757 158 GIRYVRLKPLDIfsneRRVSYE----QLLWNAFSELLGFLLPLLLAVILFLKLLEWW 210
RING-HC_PEX2 cd16526
RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as ...
242-288 1.46e-21

RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as peroxisome biogenesis factor 2, 35 kDa peroxisomal membrane protein, peroxisomal membrane protein 3, peroxisome assembly factor 1 (PAF-1), or RING finger protein 72 (RNF72), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It may be involved in the biogenesis of peroxisomes, as well as in peroxisomal matrix protein import. Mutations in the PEX2 gene are the primary defect in a subset of patients with Zellweger syndrome and related peroxisome biogenesis disorders. Moreover, PEX2 functions as an E3-ubiquitin ligase that mediates the UBC4-dependent polyubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation.


Pssm-ID: 438189 [Multi-domain]  Cd Length: 49  Bit Score: 85.51  E-value: 1.46e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1935598096 242 KECALCGEWPT-MPHTIGCEHVFCYYCVKSSFLFDMYFTCPKCGTEVH 288
Cdd:cd16526     2 TECAICGEWPTnNPYSTGCGHVYCYYCIKSNLLADDSFTCPRCGSPVS 49
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
244-283 5.59e-08

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 48.12  E-value: 5.59e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1935598096 244 CALCGEWPTMPHTI-GCEHVFCYYCVKSSfLFDMYFTCPKC 283
Cdd:pfam00097   1 CPICLEEPKDPVTLlPCGHLFCSKCIRSW-LESGNVTCPLC 40
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
244-283 2.07e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 38.26  E-value: 2.07e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1935598096  244 CALC-GEWPTMPHTIGCEHVFCYYCVKSSFLfDMYFTCPKC 283
Cdd:smart00184   1 CPIClEEYLKDPVILPCGHTFCRSCIRKWLE-SGNNTCPIC 40
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
243-288 5.67e-04

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 40.65  E-value: 5.67e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1935598096 243 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMYFTCPKCGTEVH 288
Cdd:COG5574   217 KCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262
 
Name Accession Description Interval E-value
Pex2_Pex12 pfam04757
Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of ...
27-224 2.49e-39

Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.


Pssm-ID: 398431  Cd Length: 213  Bit Score: 137.13  E-value: 2.49e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1935598096  27 KALEQLVWSQFTQCFHGFKPGLLA-RFEPEVKAFLWLFLWRFTIYSKNATVGQSVLNIQYKNDSSPnpvYQPPSKNQKLL 105
Cdd:pfam04757   2 EELESLLRPQLRYILRLLAGQRFPlNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDG---GRLLSRRRRLL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1935598096 106 YAVCTIGGRWLEERCYDLF--------RNRHLASFGKAK------QCMNFVVGLLKLGELMNFLIFLqKGKFATLTERLL 171
Cdd:pfam04757  79 SLLLLVLLPYLLRKLDSLLprlsandlESRNARDSLKSRlkryllKLYPFLESLYKLLNLHLFLFYL-TGKYYSLSKRLL 157
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1935598096 172 GIHSVFCKPQSM----REVGFEymnrELLWHGFAEFLVFLLPLINIQKLKAKLSSWC 224
Cdd:pfam04757 158 GIRYVRLKPLDIfsneRRVSYE----QLLWNAFSELLGFLLPLLLAVILFLKLLEWW 210
RING-HC_PEX2 cd16526
RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as ...
242-288 1.46e-21

RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as peroxisome biogenesis factor 2, 35 kDa peroxisomal membrane protein, peroxisomal membrane protein 3, peroxisome assembly factor 1 (PAF-1), or RING finger protein 72 (RNF72), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It may be involved in the biogenesis of peroxisomes, as well as in peroxisomal matrix protein import. Mutations in the PEX2 gene are the primary defect in a subset of patients with Zellweger syndrome and related peroxisome biogenesis disorders. Moreover, PEX2 functions as an E3-ubiquitin ligase that mediates the UBC4-dependent polyubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation.


Pssm-ID: 438189 [Multi-domain]  Cd Length: 49  Bit Score: 85.51  E-value: 1.46e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1935598096 242 KECALCGEWPT-MPHTIGCEHVFCYYCVKSSFLFDMYFTCPKCGTEVH 288
Cdd:cd16526     2 TECAICGEWPTnNPYSTGCGHVYCYYCIKSNLLADDSFTCPRCGSPVS 49
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
244-283 5.59e-08

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 48.12  E-value: 5.59e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1935598096 244 CALCGEWPTMPHTI-GCEHVFCYYCVKSSfLFDMYFTCPKC 283
Cdd:pfam00097   1 CPICLEEPKDPVTLlPCGHLFCSKCIRSW-LESGNVTCPLC 40
RING-HC_PCGF5 cd16737
RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ...
244-295 2.39e-05

RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, also known as RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438395 [Multi-domain]  Cd Length: 95  Bit Score: 42.44  E-value: 2.39e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1935598096 244 CALCGEWPTMPHTIG-CEHVFCYYCVKSSFLFDMYftCPKCGTEVHSVQPLKS 295
Cdd:cd16737    13 CRICKGYLIKPTTVTeCLHTFCKSCIVQHFEDSND--CPECGIQVHETNPLEM 63
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
243-283 2.59e-05

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 40.55  E-value: 2.59e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1935598096 243 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLfDMYFTCPKC 283
Cdd:cd16449     2 ECPICLERLKDPVLLPCGHVFCRECIRRLLE-SGSIKCPIC 41
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
243-289 1.37e-04

RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as T-cell RING activation protein 1 (TRAC-1), is an E3 ubiquitin-protein ligase that is predominantly expressed in lymphoid cells, and functions as a positive regulator of T cell activation. It also down-modulates HIV replication and inhibits pathogen-induced cytokine production. It negatively regulates type I interferon signaling, which conjugates Lys(48)-linked ubiquitination to retinoic acid-inducible gene-I (RIG-I) and subsequently leads to the proteasome-dependent degradation of RIG-I. Further, RNF125 conjugates ubiquitin to melanoma differentiation-associated gene 5 (MDA5), a family protein of RIG-I. It thus acts as a negative regulator of RIG-I signaling, and is a direct target of miR-15b in the context of Japanese encephalitis virus (JEV) infection. Moreover, RNF125 binds to and ubiquitinates JAK1, prompting its degradation and inhibition of receptor tyrosine kinase (RTK) expression. It also negatively regulates p53 function through physical interaction and ubiquitin-mediated proteasome degradation. Mutations in RNF125 may lead to overgrowth syndromes (OGS). RNF125, together with three closely related proteins: RNF114, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). The UIM of RNF125 binds K48-linked poly-ubiquitin chains and is, together with the RING domain, required for auto-ubiquitination.


Pssm-ID: 438204 [Multi-domain]  Cd Length: 50  Bit Score: 39.09  E-value: 1.37e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1935598096 243 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMYfTCPKCGTEVHS 289
Cdd:cd16542     3 DCAVCLEVLHQPVRTRCGHVFCRPCIATSLRNNTW-TCPYCRAYLSS 48
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
244-283 2.07e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 38.26  E-value: 2.07e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1935598096  244 CALC-GEWPTMPHTIGCEHVFCYYCVKSSFLfDMYFTCPKC 283
Cdd:smart00184   1 CPIClEEYLKDPVILPCGHTFCRSCIRKWLE-SGNNTCPIC 40
RING-HC_PCGF2 cd16734
RING finger found in polycomb group RING finger protein 2 (PCGF2) and similar proteins; PCGF2, ...
244-295 3.77e-04

RING finger found in polycomb group RING finger protein 2 (PCGF2) and similar proteins; PCGF2, also known as DNA-binding protein Mel-18, RING finger protein 110 (RNF110), or zinc finger protein 144 (ZNF144), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a canonical Polycomb repressive complex 1 (PRC1), which is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a Polyhomeotic protein (PHC1, PHC2, or PHC3). Like other PCGF homologs, PCGF2 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF2 uniquely regulates PRC1 to specify mesoderm cell fate in embryonic stem cells. It is required for PRC1 stability and maintenance of gene repression in embryonic stem cells (ESCs) and essential for ESC differentiation into early cardiac-mesoderm precursors. PCGF2 also plays a significant role in the angiogenic function of endothelial cells (ECs) by regulating endothelial gene expression. Furthermore, PCGF2 is a SUMO-dependent regulator of hormone receptors. It facilitates the deSUMOylation process by inhibiting PCGF4/BMI1-mediated ubiquitin-proteasomal degradation of SUMO1/sentrin-specific protease 1 (SENP1). It is also a novel negative regulator of breast cancer stem cells (CSCs) that inhibits the stem cell population and in vitro and in vivo self-renewal through the inactivation of Wnt-mediated Notch signaling. PCGF2 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438392 [Multi-domain]  Cd Length: 80  Bit Score: 38.43  E-value: 3.77e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1935598096 244 CALCGEWPTMPHTI-GCEHVFCYYCVKSSFLFDMYftCPKCGTEVHSVQPLKS 295
Cdd:cd16734    17 CALCGGYFIDAATIvECLHSFCKTCIVRYLETNKY--CPMCDVQVHKTRPLLS 67
RING-HC_TRIM41-like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
244-283 4.10e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins; TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain.


Pssm-ID: 438264 [Multi-domain]  Cd Length: 53  Bit Score: 37.60  E-value: 4.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1935598096 244 CALCGEWPTMPHTIGCEHVFCYYCVKSSFlfdmYFTCPKC 283
Cdd:cd16602     6 CAICLDYFKDPVSIGCGHNFCRVCVTQLW----GFTCPQC 41
RING-HC_PCGF6 cd16738
RING finger found in polycomb group RING finger protein 6 (PCGF6) and similar proteins; PCGF6, ...
244-293 4.89e-04

RING finger found in polycomb group RING finger protein 6 (PCGF6) and similar proteins; PCGF6, also known as Mel18 and Bmi1-like RING finger (MBLR), or RING finger protein 134 (RNF134), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like L3MBTL2 complex, which is composed of some canonical components, such as RNF2, CBX3, CXB4, CXB6, CXB7, and CXB8, as well as some noncanonical components, such as L3MBTL2, E2F6, WDR5, HDAC1, and RYBP, and plays a critical role in epigenetic transcriptional silencing in higher eukaryotes. Like other PCGF homologs, PCGF6 possesses the transcriptional repression activity, and also associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF6 can regulate the enzymatic activity of JARID1d/KDM5D, a trimethyl H3K4 demethylase, through direct interaction. Furthermore, PCGF6 is expressed predominantly in meiotic and post-meiotic male germ cells and may play important roles in mammalian male germ cell development. It also regulates mesodermal lineage differentiation in mammalian embryonic stem cells (ESCs) and functions in induced pluripotent stem (iPS) reprogramming. The activity of PCGF6 is found to be regulated by cell cycle dependent phosphorylation. PCGF6 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438396 [Multi-domain]  Cd Length: 59  Bit Score: 37.59  E-value: 4.89e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1935598096 244 CALCGEWPTMPHTIG-CEHVFCYYCVKSSFLFDMyfTCPKCGTEVHSVQPL 293
Cdd:cd16738    10 CSICKGYFIDATTITeCLHTFCKSCIVRHFYYSN--RCPKCNIVVHQTQPL 58
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
243-288 5.67e-04

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 40.65  E-value: 5.67e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1935598096 243 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMYFTCPKCGTEVH 288
Cdd:COG5574   217 KCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
244-283 5.83e-04

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438263 [Multi-domain]  Cd Length: 44  Bit Score: 37.08  E-value: 5.83e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1935598096 244 CALCGEWPTMPHTIGCEHVFCYYCVKSSFL-FDMYFTCPKC 283
Cdd:cd16601     4 CSLCKEYLKDPVIIECGHNFCRACITRFWEeLDGDFPCPQC 44
RING-HC_RNF146 cd16546
RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; ...
243-287 1.51e-03

RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; RNF146, also known as dactylidin, or iduna, is a cytoplasmic E3 ubiquitin-protein ligase that is responsible for PARylation-dependent ubiquitination (PARdU). It displays neuroprotective property due to its inhibition of Parthanatos, a PAR dependent cell death, via binding with Poly(ADP-ribose) (PAR). It also modulates PAR polymerase-1 (PARP-1)-mediated oxidative cell injury in cardiac myocytes. Moreover, RNF146 mediates tankyrase-dependent degradation of axin, thereby positively regulating Wnt signaling. It also facilitates DNA repair and protects against cell death induced by DNA damaging agents or gamma-irradiation by translocating to the nucleus after cellular injury and promoting the ubiquitination and degradation of various nuclear proteins involved in DNA damage repair. Furthermore, RNF146 is implicated in neurodegenerative disease and cancer development. It regulates the development and progression of non-small cell lung cancer (NSCLC) by enhancing cell growth, invasion, and survival. RNF146 contains an N-terminal C3HC4-type RING-HC finger followed by a WWE domain with a poly(ADP-ribose) (PAR) binding motif at the tail.


Pssm-ID: 438208 [Multi-domain]  Cd Length: 50  Bit Score: 35.82  E-value: 1.51e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1935598096 243 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMyfTCPKCGTEV 287
Cdd:cd16546     2 ECPICLQTCIHPVKLPCGHIFCYLCVKGVAWQSK--RCALCRQEI 44
RING-HC_HAKAI-like cd16508
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Hakai, zinc finger protein 645 ...
257-296 3.08e-03

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Hakai, zinc finger protein 645 (ZNF645), and similar proteins; Hakai, also known as Casitas B-lineage lymphoma-transforming sequence-like protein 1, RING finger protein 188 (RNF188), or c-Cbl-like protein 1 (CBLL1), is an E3 ubiquitin ligase that disrupts cell-cell contacts in epithelial cells and is upregulated in human colon and gastric adenocarcinomas. It was identified to mediate the posttranslational downregulation of E-cadherin (CDH1), a major component of adherens junctions in epithelial cells and a potent tumor suppressor. It also promotes ubiquitination of several other tyrosine-phosphorylated Src substrates, including cortactin (CTTN) and DOK1. Hakai acts as a homodimer arranged in an anti-parallel configuration with a novel HYB (Hakai pTyr-binding) domain that forms a phosphotyrosine-binding pocket. Each monomer contains a C3HC4-type RING-HC finger and a short pTyr-B domain that incorporates a novel, atypical C2H2-type Zn-finger coordination motif. Both domains are important for dimerization. ZNF645 is a novel testis-specific E3 ubiquitin-protein ligase that plays a role in sperm production and quality control. It has a structure similar to that of the c-Cbl-like protein Hakai. In contrast to Hakai, its HYB domain demonstrates different target specificities. It interacts with v-Src-phosphorylated E-cadherin, but not to cortactin.


Pssm-ID: 438171 [Multi-domain]  Cd Length: 51  Bit Score: 35.01  E-value: 3.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1935598096 257 IGCEHVFCYYCVKSSflfdmYFTCPKCGTEVHSVQPLKSG 296
Cdd:cd16508    17 IPCKHVFCLDCARLH-----DKICPRCDDPVQRIEQCTRG 51
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
243-287 4.03e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 35.04  E-value: 4.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1935598096 243 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMYFTCPKCGTEV 287
Cdd:cd16568     6 ECIICHEYLYEPMVTTCGHTYCYTCLNTWFKSNRSLSCPDCRTKI 50
RING-HC_RNFT1 cd16741
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 ...
230-285 5.62e-03

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 (RNFT1); RNFT1, also known as protein PTD016, is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear.


Pssm-ID: 438399 [Multi-domain]  Cd Length: 58  Bit Score: 34.48  E-value: 5.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1935598096 230 TAGSDSTLGSSGKECALCGEWPTMPHTIGCEHVFCYYCVksSFLFDMYFTCPKCGT 285
Cdd:cd16741     3 IAASKRQCSEADDICAICQAEFRKPILLICQHVFCEECI--SLWFNREKTCPLCRT 56
RING-HC_UHRF cd16613
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
243-286 6.97e-03

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438275 [Multi-domain]  Cd Length: 46  Bit Score: 33.87  E-value: 6.97e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1935598096 243 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDmYFTCPKCGTE 286
Cdd:cd16613     2 TCICCQELVYKPITTPCKHNICKSCLQRSFKAE-VYTCPACRHD 44
RING-HC_CHR27-like cd23142
RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ...
244-287 7.08e-03

RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) and similar proteins; CHR27, also called protein SNF2-RING-HELICASE-LIKE 1, is a probable helicase-like transcription factor involved in transcriptional gene silencing. It associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. It may be involved in nucleosome positioning to form ordered nucleosome arrays on chromatin. It associates with SUVR2 and functions redundantly with FRG2. It is required for the efficient methylation of a broad range of RdDM target loci. CHR27 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438504 [Multi-domain]  Cd Length: 55  Bit Score: 34.08  E-value: 7.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1935598096 244 CALCGEWPTMPHTIGCEHVFCYYCV----KSSFLFDMYFTCPKCGTEV 287
Cdd:cd23142     3 CPICNDPPEDAVVTLCGHVFCCECVfqylSSDRTCRQFNHCPLCRQKL 50
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
244-283 7.23e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438271 [Multi-domain]  Cd Length: 58  Bit Score: 34.27  E-value: 7.23e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1935598096 244 CALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMY--FTCPKC 283
Cdd:cd16609     6 CSICLGLYQDPVTLPCQHSFCRACIEDHWRQKDEgsFSCPEC 47
RING-HC_PCGF4 cd16736
RING finger found in polycomb group RING finger protein 4 (PCGF4) and similar proteins; PCGF4, ...
244-293 8.17e-03

RING finger found in polycomb group RING finger protein 4 (PCGF4) and similar proteins; PCGF4, also known as polycomb complex protein BMI-1 (B cell-specific Moloney murine leukemia virus integration site 1) or RING finger protein 51 (RNF51), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a canonical Polycomb repressive complex 1 (PRC1), which is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a Polyhomeotic protein (PHC1, PHC2, or PHC3), and plays important roles in chromatin compaction and H2AK119 monoubiquitination. PCGF4 associates with the Runx1/CBFbeta transcription factor complex to silence target genes in a PRC2-independent manner. Moreover, PCGF4 is expressed in the hair cells and supporting cells. It can regulate cell survival by controlling mitochondrial function and reactive oxygen species (ROS) level in thymocytes and neurons, thus having an important role in the survival and sensitivity to ototoxic drug of auditory hair cells. Furthermore, PCGF4 controls memory CD4 T-cell survival through direct repression of Noxa gene in an Ink4a- and Arf-independent manner. It is required in neurons to suppress p53-induced apoptosis via regulating the antioxidant defensive response, and also involved in the tumorigenesis of various cancer types. PCGF4 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438394 [Multi-domain]  Cd Length: 97  Bit Score: 35.37  E-value: 8.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1935598096 244 CALCGEWPTMPHTI-GCEHVFCYYCVKSSFLFDMYftCPKCGTEVHSVQPL 293
Cdd:cd16736    14 CVLCGGYFIDATTIiECLHSFCKTCIVRYLETSKY--CPICDVQVHKTRPL 62
RING-HC_RNFT2 cd16742
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2 ...
238-287 9.53e-03

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2(RNFT2); RNFT2, also known as transmembrane protein 118 (TMEM118), is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear.


Pssm-ID: 438400 [Multi-domain]  Cd Length: 67  Bit Score: 34.08  E-value: 9.53e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1935598096 238 GSSGKECALCGEWPTMPHTIGCEHVFCYYCVksSFLFDMYFTCPKCGTEV 287
Cdd:cd16742    10 SEAGDICAICQAEFREPLILICQHVFCEECL--CLWFDRERTCPLCRSVV 57
RING-HC_RNFT1-like cd16532
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein ...
244-283 9.60e-03

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein RNFT1, RNFT2, and similar proteins; Both RNFT1 and RNFT2 are multi-pass membrane proteins containing a C3HC4-type RING-HC finger. Their biological roles remain unclear.


Pssm-ID: 438194 [Multi-domain]  Cd Length: 41  Bit Score: 33.43  E-value: 9.60e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1935598096 244 CALCGEWPTMPHTIGCEHVFCYYCVksSFLFDMYFTCPKC 283
Cdd:cd16532     3 CPICQDEFKDPVVLRCKHIFCEDCV--SEWFERERTCPLC 40
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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