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Conserved domains on  [gi|21717826|ref|NP_663629|]
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RAD52 motif-containing protein 1 isoform 1 [Homo sapiens]

Protein Classification

RNA-binding protein( domain architecture ID 10188893)

RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_RDM1 cd12364
RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar ...
 15-95 5.28e-44

RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins; This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA.


:

Pssm-ID: 409799 [Multi-domain]  Cd Length: 81  Bit Score: 144.43  E-value: 5.28e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21717826  15 KTLLVWELSSGPTAEALHHSLFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKSPVKVR 94
Cdd:cd12364   1 KTLFVWNISPKLTEEEIYESLCKAFSAFGLLYSVRVFPNAAVATPGFYAFVKFYSARDASRAQKALNGKWLFQGSPLKVR 80


                .
gi 21717826  95 L 95
Cdd:cd12364  81 F 81
 
Name Accession Description Interval E-value
RRM_RDM1 cd12364
RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar ...
 15-95 5.28e-44

RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins; This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA.


Pssm-ID: 409799 [Multi-domain]  Cd Length: 81  Bit Score: 144.43  E-value: 5.28e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21717826  15 KTLLVWELSSGPTAEALHHSLFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKSPVKVR 94
Cdd:cd12364   1 KTLFVWNISPKLTEEEIYESLCKAFSAFGLLYSVRVFPNAAVATPGFYAFVKFYSARDASRAQKALNGKWLFQGSPLKVR 80


                .
gi 21717826  95 L 95
Cdd:cd12364  81 F 81
RRM smart00360
RNA recognition motif;
35-93 6.48e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.27  E-value: 6.48e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 21717826     35 LFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKsPVKV 93
Cdd:smart00360  16 LRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGR-PLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 35-88 3.23e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 38.37  E-value: 3.23e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 21717826    35 LFTAFSQFGLLYSVRVFPNAAVAHPGFyAVIKFYSARAAHRAQKACDRKQLFQK 88
Cdd:pfam00076  15 LKDLFSKFGPIKSIRLVRDETGRSKGF-AFVEFEDEEDAEKAIEALNGKELGGR 67
 
Name Accession Description Interval E-value
RRM_RDM1 cd12364
RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar ...
 15-95 5.28e-44

RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins; This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA.


Pssm-ID: 409799 [Multi-domain]  Cd Length: 81  Bit Score: 144.43  E-value: 5.28e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21717826  15 KTLLVWELSSGPTAEALHHSLFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKSPVKVR 94
Cdd:cd12364   1 KTLFVWNISPKLTEEEIYESLCKAFSAFGLLYSVRVFPNAAVATPGFYAFVKFYSARDASRAQKALNGKWLFQGSPLKVR 80


                .
gi 21717826  95 L 95
Cdd:cd12364  81 F 81
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 17-94 3.96e-07

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 46.51  E-value: 3.96e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21717826  17 LLVWELSSGPTAEALHHslftAFSQFGLLYSVRVFPNAAVAHPGfYAVIKFYSARAAHRAQKACDRKQlFQKSPVKVR 94
Cdd:cd00590   1 LFVGNLPPDTTEEDLRE----LFSKFGEVVSVRIVRDRDGKSKG-FAFVEFESPEDAEKALEALNGTE-LGGRPLKVS 72
RRM smart00360
RNA recognition motif;
35-93 6.48e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.27  E-value: 6.48e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 21717826     35 LFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKsPVKV 93
Cdd:smart00360  16 LRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGR-PLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 35-88 3.23e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 38.37  E-value: 3.23e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 21717826    35 LFTAFSQFGLLYSVRVFPNAAVAHPGFyAVIKFYSARAAHRAQKACDRKQLFQK 88
Cdd:pfam00076  15 LKDLFSKFGPIKSIRLVRDETGRSKGF-AFVEFEDEEDAEKAIEALNGKELGGR 67
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
 16-88 2.52e-03

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409948 [Multi-domain]  Cd Length: 71  Bit Score: 35.95  E-value: 2.52e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21717826  16 TLLVWELSSGPTAEALHhslfTAFSQFGLLYSVRVFPNAAvahpgFYAVIKFYSARAAHRAQKACDRKQLFQK 88
Cdd:cd12529   3 TLVVFNLDPSISNDDLH----QIFGAYGEIKEIRETPNKR-----HHKFIEFYDVRSAEAALKALNKSEIAGK 66
RRM1_Spen cd12308
RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily ...
 14-93 2.85e-03

RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily corresponds to the RRM1 domain in the Spen (split end) family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also known as one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong- to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409749 [Multi-domain]  Cd Length: 78  Bit Score: 36.07  E-value: 2.85e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21717826  14 DKTLLVWELSSGPTAEALHHSLFTAFSQFGLLySVRV--FPNAAVAHpgfyavIKFYSARAAHRAQKACDRKQLFQKsPV 91
Cdd:cd12308   1 YKTLCVSNLPAKLSDEEIEDVLYHEFKKFGDV-SVRLqhDGDERVAY------VNFRHPEDAREAKHAKLRLVLFDR-PL 72


                ..
gi 21717826  92 KV 93
Cdd:cd12308  73 NV 74
 
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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