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Conserved domains on  [gi|172046830|sp|Q52KJ8|]
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RecName: Full=Methionine-R-sulfoxide reductase B1; Short=MsrB1; AltName: Full=Selenoprotein X; Short=SelX

Protein Classification

peptide-methionine (R)-S-oxide reductase( domain architecture ID 81886)

peptide-methionine (R)-S-oxide reductase catalyzes the reduction of methionine sulfoxide (MetSO) to methionine in proteins

CATH:  2.170.150.20
EC:  1.8.4.12
Gene Ontology:  GO:0046872|GO:0033743|GO:0030091|GO:0034599
PubMed:  11169920
SCOP:  4002166

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SelR super family cl15841
SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate ...
 14-108 4.26e-26

SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.


The actual alignment was detected with superfamily member COG0229:

Pssm-ID: 472838  Cd Length: 133  Bit Score: 94.38  E-value: 4.26e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830  14 NHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHEDSVAkcpEK-------NRPEalkVSCGKCGNGLGHEFlNDG 86
Cdd:COG0229   39 DNKEEGIYVCAGCGAPLFSSDTKFDSGTGWPSFTKPIDPGAVE---EKedrshgmVRTE---VRCARCGAHLGHVF-DDG 111

                         90       100
                 ....*....|....*....|...
gi 172046830  87 PK-RGQsRFUIFSSSLKFIPKGK 108
Cdd:COG0229  112 PPpTGL-RYCINSAALRFIPKEE 133
 
Name Accession Description Interval E-value
MsrB COG0229
Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, ...
 14-108 4.26e-26

Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 439999  Cd Length: 133  Bit Score: 94.38  E-value: 4.26e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830  14 NHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHEDSVAkcpEK-------NRPEalkVSCGKCGNGLGHEFlNDG 86
Cdd:COG0229   39 DNKEEGIYVCAGCGAPLFSSDTKFDSGTGWPSFTKPIDPGAVE---EKedrshgmVRTE---VRCARCGAHLGHVF-DDG 111

                         90       100
                 ....*....|....*....|...
gi 172046830  87 PK-RGQsRFUIFSSSLKFIPKGK 108
Cdd:COG0229  112 PPpTGL-RYCINSAALRFIPKEE 133
SelR pfam01641
SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate ...
 7-105 1.48e-25

SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.


Pssm-ID: 460278  Cd Length: 120  Bit Score: 92.42  E-value: 1.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830    7 FGGEvFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHEDSVAKCPEKN----RPEalkVSCGKCGNGLGHEF 82
Cdd:pfam01641  23 FTGE-YWDNKEPGIYVCAGCGTPLFSSDTKFDSGCGWPSFYDPIPGDAVKEKEDTShgmvRTE---VRCARCGGHLGHVF 98

                          90       100
                  ....*....|....*....|....
gi 172046830   83 lNDGPK-RGQsRFUIFSSSLKFIP 105
Cdd:pfam01641  99 -DDGPPpTGL-RYCINSASLKFIP 120
TIGR00357 TIGR00357
methionine-R-sulfoxide reductase; This model describes a domain found in PilB, a protein ...
 14-106 5.16e-24

methionine-R-sulfoxide reductase; This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested. [Protein fate, Protein modification and repair, Cellular processes, Adaptations to atypical conditions]


Pssm-ID: 129454  Cd Length: 134  Bit Score: 89.06  E-value: 5.16e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830   14 NHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHEDSVAKCPEKN----RPEalkVSCGKCGNGLGHEFlNDGPKR 89
Cdd:TIGR00357  34 DNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDEShgmiRTE---VRCRNCDAHLGHVF-DDGPEP 109

                          90
                  ....*....|....*..
gi 172046830   90 GQSRFUIFSSSLKFIPK 106
Cdd:TIGR00357 110 TGLRYCINSAALKFIPL 126
PRK05550 PRK05550
bifunctional methionine sulfoxide reductase B/A protein; Provisional
 7-114 9.26e-22

bifunctional methionine sulfoxide reductase B/A protein; Provisional


Pssm-ID: 235499 [Multi-domain]  Cd Length: 283  Bit Score: 86.49  E-value: 9.26e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830   7 FGGEvFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIhEDSVAKCPEKN--RPEalkVSCGKCGNGLGHEFLN 84
Cdd:PRK05550  24 FSGE-YYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEI-PGAVKRLPDADgrRTE---IVCANCGAHLGHVFEG 98

                         90       100       110
                 ....*....|....*....|....*....|
gi 172046830  85 DGPKRGQSRFUIFSSSLKFIPKGKEAPASQ 114
Cdd:PRK05550  99 EGLTPKNTRHCVNSASLDFVPAEEGAYDTE 128
 
Name Accession Description Interval E-value
MsrB COG0229
Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, ...
 14-108 4.26e-26

Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 439999  Cd Length: 133  Bit Score: 94.38  E-value: 4.26e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830  14 NHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHEDSVAkcpEK-------NRPEalkVSCGKCGNGLGHEFlNDG 86
Cdd:COG0229   39 DNKEEGIYVCAGCGAPLFSSDTKFDSGTGWPSFTKPIDPGAVE---EKedrshgmVRTE---VRCARCGAHLGHVF-DDG 111

                         90       100
                 ....*....|....*....|...
gi 172046830  87 PK-RGQsRFUIFSSSLKFIPKGK 108
Cdd:COG0229  112 PPpTGL-RYCINSAALRFIPKEE 133
SelR pfam01641
SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate ...
 7-105 1.48e-25

SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.


Pssm-ID: 460278  Cd Length: 120  Bit Score: 92.42  E-value: 1.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830    7 FGGEvFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHEDSVAKCPEKN----RPEalkVSCGKCGNGLGHEF 82
Cdd:pfam01641  23 FTGE-YWDNKEPGIYVCAGCGTPLFSSDTKFDSGCGWPSFYDPIPGDAVKEKEDTShgmvRTE---VRCARCGGHLGHVF 98

                          90       100
                  ....*....|....*....|....
gi 172046830   83 lNDGPK-RGQsRFUIFSSSLKFIP 105
Cdd:pfam01641  99 -DDGPPpTGL-RYCINSASLKFIP 120
TIGR00357 TIGR00357
methionine-R-sulfoxide reductase; This model describes a domain found in PilB, a protein ...
 14-106 5.16e-24

methionine-R-sulfoxide reductase; This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested. [Protein fate, Protein modification and repair, Cellular processes, Adaptations to atypical conditions]


Pssm-ID: 129454  Cd Length: 134  Bit Score: 89.06  E-value: 5.16e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830   14 NHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHEDSVAKCPEKN----RPEalkVSCGKCGNGLGHEFlNDGPKR 89
Cdd:TIGR00357  34 DNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDEShgmiRTE---VRCRNCDAHLGHVF-DDGPEP 109

                          90
                  ....*....|....*..
gi 172046830   90 GQSRFUIFSSSLKFIPK 106
Cdd:TIGR00357 110 TGLRYCINSAALKFIPL 126
PRK05550 PRK05550
bifunctional methionine sulfoxide reductase B/A protein; Provisional
 7-114 9.26e-22

bifunctional methionine sulfoxide reductase B/A protein; Provisional


Pssm-ID: 235499 [Multi-domain]  Cd Length: 283  Bit Score: 86.49  E-value: 9.26e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830   7 FGGEvFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIhEDSVAKCPEKN--RPEalkVSCGKCGNGLGHEFLN 84
Cdd:PRK05550  24 FSGE-YYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEI-PGAVKRLPDADgrRTE---IVCANCGAHLGHVFEG 98

                         90       100       110
                 ....*....|....*....|....*....|
gi 172046830  85 DGPKRGQSRFUIFSSSLKFIPKGKEAPASQ 114
Cdd:PRK05550  99 EGLTPKNTRHCVNSASLDFVPAEEGAYDTE 128
PRK05508 PRK05508
methionine-R-sulfoxide reductase;
7-108 1.61e-19

methionine-R-sulfoxide reductase;


Pssm-ID: 180121  Cd Length: 119  Bit Score: 77.06  E-value: 1.61e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830   7 FGGEvFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIhEDSVAKCPEKN--RPEALkvsCGKCGNGLGHEFLN 84
Cdd:PRK05508  21 FSGE-YNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEI-KGAVKRIPDADgrRTEIV---CANCGGHLGHVFEG 95

                         90       100
                 ....*....|....*....|....
gi 172046830  85 DGPKRGQSRFUIFSSSLKFIPKGK 108
Cdd:PRK05508  96 EGFTPKNTRHCVNSISLKFVPDKG 119
PRK14018 PRK14018
bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide ...
 12-108 5.77e-15

bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB;


Pssm-ID: 184456 [Multi-domain]  Cd Length: 521  Bit Score: 69.13  E-value: 5.77e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 172046830  12 FQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHEDSVAKCPEK----NRPEalkVSCGKCGNGLGHEFlNDGP 87
Cdd:PRK14018 410 YDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKVVTEHDDFsynmRRTE---VRSRAADSHLGHVF-PDGP 485

                         90       100
                 ....*....|....*....|..
gi 172046830  88 K-RGQSRFUIFSSSLKFIPKGK 108
Cdd:PRK14018 486 RdKGGLRYCINGASLKFIPLEQ 507
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 19-77 1.55e-03

DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441202 [Multi-domain]  Cd Length: 103  Bit Score: 35.31  E-value: 1.55e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 172046830  19 GVYVCAKCGYELFSSRSKYAhsspwpAFTETI-HEDS----VAKCPEKNRPEAlKVSCGKCGNG 77
Cdd:COG1594   15 GVLVCPKCGYEEPRDEEAEA------KYVSTEeQEDKeiivVEEEEVEGLPTT-KVICPKCGND 71
 
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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