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Conserved domains on  [gi|2217301653|ref|XP_047288656|]
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ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X8 [Homo sapiens]

Protein Classification

MINDY family deubiquitinase( domain architecture ID 10516731)

MINDY family deubiquitinase similar to Homo sapiens ubiquitin carboxyl-terminal hydrolase MINDY-1 that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins

EC:  3.4.19.12
Gene Ontology:  GO:0004843|GO:1990380

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MINDY_DUB pfam04424
MINDY deubiquitinase; This entry represents a group of deubiquitinating (DUB) enzymes known as ...
 279-392 4.31e-40

MINDY deubiquitinase; This entry represents a group of deubiquitinating (DUB) enzymes known as the MINDY family (MIU-containing novel DUB). Ubiquitin (Ub) is released one molecule at a time from the distal end of proteins with Lys48-linked polyubiquitin chains. Long polyubiquitin chains are preferred. The catalytic Cys and His residues have been identified by site-directed mutagenesis, as has the Gln that participates in formation of the oxyanion hole during catalysis. Despite the structural similarity to papain-like cysteine peptidases, a residue corresponding to the Asn that orientates the imidazolium ring of the catalytic His has not been identified. Members of the MINDY family of DUBs contain an MIU (motif interacting with Ub) motif, which is a helical motif that binds mono-Ub.


:

Pssm-ID: 461303  Cd Length: 110  Bit Score: 141.14  E-value: 4.31e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653 279 WKVKLPPMMEIITAEQLMEYLGDYMLDAKPkeiseiqrLNYEQihhccrfkkssktlkgknNMSDAMAILHKLQTGLDVN 358
Cdd:pfam04424   7 GKIELLPDRETISLEDLLELLADYLLDNNP--------LNYEQ------------------NISDALSLLPKLQTGLDVN 60

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2217301653 359 VRFTGVRVFEYTPECIVFDLLDIPLYHGWLVDPQ 392
Cdd:pfam04424  61 PRFTGVTSFEDTPELALFDLLNIPLVHGWLVDPQ 94
PRK07003 super family cl35530
DNA polymerase III subunit gamma/tau;
19-209 2.59e-03

DNA polymerase III subunit gamma/tau;


The actual alignment was detected with superfamily member PRK07003:

Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 40.60  E-value: 2.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653  19 PASGTGSSQEGLQETRL-------AAGDGPGVWAAETSGGNGLGAAAARRSLPDSASPAGSPEVPGPCSSSAGLDLKDSG 91
Cdd:PRK07003  360 PAVTGGGAPGGGVPARVagavpapGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRG 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653  92 lESPAAAEAPLRGQYKVTASPETAVAgvghELGTAGDAGARPDLAGTCQAELTAAGSEEPsSAGGLSSSCSDPSPPGESP 171
Cdd:PRK07003  440 -DDAADGDAPVPAKANARASADSRCD----ERDAQPPADSGSASAPASDAPPDAAFEPAP-RAAAPSAATPAAVPDARAP 513

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2217301653 172 SLDSLESFSNLHSFPSScEFNSEEGAENRVPEEEEGAA 209
Cdd:PRK07003  514 AAASREDAPAAAAPPAP-EARPPTPAAAAPAARAGGAA 550
 
Name Accession Description Interval E-value
MINDY_DUB pfam04424
MINDY deubiquitinase; This entry represents a group of deubiquitinating (DUB) enzymes known as ...
 279-392 4.31e-40

MINDY deubiquitinase; This entry represents a group of deubiquitinating (DUB) enzymes known as the MINDY family (MIU-containing novel DUB). Ubiquitin (Ub) is released one molecule at a time from the distal end of proteins with Lys48-linked polyubiquitin chains. Long polyubiquitin chains are preferred. The catalytic Cys and His residues have been identified by site-directed mutagenesis, as has the Gln that participates in formation of the oxyanion hole during catalysis. Despite the structural similarity to papain-like cysteine peptidases, a residue corresponding to the Asn that orientates the imidazolium ring of the catalytic His has not been identified. Members of the MINDY family of DUBs contain an MIU (motif interacting with Ub) motif, which is a helical motif that binds mono-Ub.


Pssm-ID: 461303  Cd Length: 110  Bit Score: 141.14  E-value: 4.31e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653 279 WKVKLPPMMEIITAEQLMEYLGDYMLDAKPkeiseiqrLNYEQihhccrfkkssktlkgknNMSDAMAILHKLQTGLDVN 358
Cdd:pfam04424   7 GKIELLPDRETISLEDLLELLADYLLDNNP--------LNYEQ------------------NISDALSLLPKLQTGLDVN 60

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2217301653 359 VRFTGVRVFEYTPECIVFDLLDIPLYHGWLVDPQ 392
Cdd:pfam04424  61 PRFTGVTSFEDTPELALFDLLNIPLVHGWLVDPQ 94
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
19-209 2.59e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 40.60  E-value: 2.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653  19 PASGTGSSQEGLQETRL-------AAGDGPGVWAAETSGGNGLGAAAARRSLPDSASPAGSPEVPGPCSSSAGLDLKDSG 91
Cdd:PRK07003  360 PAVTGGGAPGGGVPARVagavpapGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRG 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653  92 lESPAAAEAPLRGQYKVTASPETAVAgvghELGTAGDAGARPDLAGTCQAELTAAGSEEPsSAGGLSSSCSDPSPPGESP 171
Cdd:PRK07003  440 -DDAADGDAPVPAKANARASADSRCD----ERDAQPPADSGSASAPASDAPPDAAFEPAP-RAAAPSAATPAAVPDARAP 513

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2217301653 172 SLDSLESFSNLHSFPSScEFNSEEGAENRVPEEEEGAA 209
Cdd:PRK07003  514 AAASREDAPAAAAPPAP-EARPPTPAAAAPAARAGGAA 550
 
Name Accession Description Interval E-value
MINDY_DUB pfam04424
MINDY deubiquitinase; This entry represents a group of deubiquitinating (DUB) enzymes known as ...
 279-392 4.31e-40

MINDY deubiquitinase; This entry represents a group of deubiquitinating (DUB) enzymes known as the MINDY family (MIU-containing novel DUB). Ubiquitin (Ub) is released one molecule at a time from the distal end of proteins with Lys48-linked polyubiquitin chains. Long polyubiquitin chains are preferred. The catalytic Cys and His residues have been identified by site-directed mutagenesis, as has the Gln that participates in formation of the oxyanion hole during catalysis. Despite the structural similarity to papain-like cysteine peptidases, a residue corresponding to the Asn that orientates the imidazolium ring of the catalytic His has not been identified. Members of the MINDY family of DUBs contain an MIU (motif interacting with Ub) motif, which is a helical motif that binds mono-Ub.


Pssm-ID: 461303  Cd Length: 110  Bit Score: 141.14  E-value: 4.31e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653 279 WKVKLPPMMEIITAEQLMEYLGDYMLDAKPkeiseiqrLNYEQihhccrfkkssktlkgknNMSDAMAILHKLQTGLDVN 358
Cdd:pfam04424   7 GKIELLPDRETISLEDLLELLADYLLDNNP--------LNYEQ------------------NISDALSLLPKLQTGLDVN 60

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2217301653 359 VRFTGVRVFEYTPECIVFDLLDIPLYHGWLVDPQ 392
Cdd:pfam04424  61 PRFTGVTSFEDTPELALFDLLNIPLVHGWLVDPQ 94
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
19-209 2.59e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 40.60  E-value: 2.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653  19 PASGTGSSQEGLQETRL-------AAGDGPGVWAAETSGGNGLGAAAARRSLPDSASPAGSPEVPGPCSSSAGLDLKDSG 91
Cdd:PRK07003  360 PAVTGGGAPGGGVPARVagavpapGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRG 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217301653  92 lESPAAAEAPLRGQYKVTASPETAVAgvghELGTAGDAGARPDLAGTCQAELTAAGSEEPsSAGGLSSSCSDPSPPGESP 171
Cdd:PRK07003  440 -DDAADGDAPVPAKANARASADSRCD----ERDAQPPADSGSASAPASDAPPDAAFEPAP-RAAAPSAATPAAVPDARAP 513

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2217301653 172 SLDSLESFSNLHSFPSScEFNSEEGAENRVPEEEEGAA 209
Cdd:PRK07003  514 AAASREDAPAAAAPPAP-EARPPTPAAAAPAARAGGAA 550
 
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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