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Conserved domains on  [gi|1958660239|ref|XP_038942500|]
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SCO cytochrome oxidase deficient homolog 1 isoform X1 [Rattus norvegicus]

Protein Classification

SCO family protein( domain architecture ID 10121908)

SCO (Synthesis of Cytochrome c Oxidase) family protein belonging to the thioredoxin superfamily, similar to mitochondrial SCO1 and SCO2 that function as copper chaperones required for the maturation and proper assembly of cytochrome c oxidase

CATH:  3.40.30.10
Gene Ontology:  GO:0046872
PubMed:  10954195|10049365|15558583
SCOP:  3000031

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SCO cd02968
SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to ...
 25-167 3.42e-66

SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properties of Sco1 implies that it participates in signaling events rather than functioning as a chaperone that transfers copper to COX II.


:

Pssm-ID: 239266  Cd Length: 142  Bit Score: 199.37  E-value: 3.42e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  25 LGGPFSLTTHNGEPKTDKDFLGQWVLIYFGFTHCPDICPEELEKMIEVVEEIDSIPsLPNLTPLFITIDPERDTKEAIAT 104
Cdd:cd02968     1 IGPDFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADG-GDDVQVVFISVDPERDTPEVLKA 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958660239 105 YVKEFSPKLVGLTGTKEEIDGVARAYRVYYSPGPKDeDEDYIVDHTIIMYLIGPDGEFLDYFG 167
Cdd:cd02968    80 YAKAFGPGWIGLTGTPEEIEALAKAFGVYYEKVPED-DGDYLVDHSAAIYLVDPDGKLVRYYG 141
 
Name Accession Description Interval E-value
SCO cd02968
SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to ...
 25-167 3.42e-66

SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properties of Sco1 implies that it participates in signaling events rather than functioning as a chaperone that transfers copper to COX II.


Pssm-ID: 239266  Cd Length: 142  Bit Score: 199.37  E-value: 3.42e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  25 LGGPFSLTTHNGEPKTDKDFLGQWVLIYFGFTHCPDICPEELEKMIEVVEEIDSIPsLPNLTPLFITIDPERDTKEAIAT 104
Cdd:cd02968     1 IGPDFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADG-GDDVQVVFISVDPERDTPEVLKA 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958660239 105 YVKEFSPKLVGLTGTKEEIDGVARAYRVYYSPGPKDeDEDYIVDHTIIMYLIGPDGEFLDYFG 167
Cdd:cd02968    80 YAKAFGPGWIGLTGTPEEIEALAKAFGVYYEKVPED-DGDYLVDHSAAIYLVDPDGKLVRYYG 141
SCO1-SenC pfam02630
SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. ...
 26-162 5.49e-65

SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus.


Pssm-ID: 460630  Cd Length: 134  Bit Score: 195.86  E-value: 5.49e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  26 GGPFSLTTHNGEPKTDKDFLGQWVLIYFGFTHCPDICPEELEKMIEVVEEIDsiPSLPNLTPLFITIDPERDTKEAIATY 105
Cdd:pfam02630   1 GGPFELVDQDGKAVTEADFEGRPSLVFFGFTHCPDVCPTTLPNMAQVLDALG--EEGIDVQPVFITVDPERDTPEVLAEY 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958660239 106 VKEFSPKLVGLTGTKEEIDGVARAYRVYYSPGPkDEDEDYIVDHTIIMYLIGPDGEF 162
Cdd:pfam02630  79 LEAFGPRIIGLTGSPEQIAAAARAFRVYYEKVP-DDGGDYTVDHTASVYLVDPDGRF 134
Sco1 COG1999
Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, ...
 30-185 8.05e-53

Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441602  Cd Length: 156  Bit Score: 165.84  E-value: 8.05e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  30 SLTTHNGEPKTDKDFLGQWVLIYFGFTHCPDICPEELEKMIEVVEEIDSIPSlPNLTPLFITIDPERDTKEAIATYVKEF 109
Cdd:COG1999     4 TLTDQDGKPVTLADLRGKPVLVFFGYTSCPDVCPTTLANLAQVQEALGEDGG-DDVQVLFISVDPERDTPEVLKAYAEAF 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958660239 110 S-PKLVGLTGTKEEIDGVARAYRVYYSpgpKDEDEDYIVDHTIIMYLIGPDGEFLDYFGQNKKKAEIAGSIAAHMRS 185
Cdd:COG1999    83 GaPRWIGLTGDPEEIAALAKAFGVYYE---KVPDGDYTFDHSAAVYLVDPDGRLRGYYPAGEDPEELAADLKALLEE 156
 
Name Accession Description Interval E-value
SCO cd02968
SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to ...
 25-167 3.42e-66

SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properties of Sco1 implies that it participates in signaling events rather than functioning as a chaperone that transfers copper to COX II.


Pssm-ID: 239266  Cd Length: 142  Bit Score: 199.37  E-value: 3.42e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  25 LGGPFSLTTHNGEPKTDKDFLGQWVLIYFGFTHCPDICPEELEKMIEVVEEIDSIPsLPNLTPLFITIDPERDTKEAIAT 104
Cdd:cd02968     1 IGPDFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADG-GDDVQVVFISVDPERDTPEVLKA 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958660239 105 YVKEFSPKLVGLTGTKEEIDGVARAYRVYYSPGPKDeDEDYIVDHTIIMYLIGPDGEFLDYFG 167
Cdd:cd02968    80 YAKAFGPGWIGLTGTPEEIEALAKAFGVYYEKVPED-DGDYLVDHSAAIYLVDPDGKLVRYYG 141
SCO1-SenC pfam02630
SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. ...
 26-162 5.49e-65

SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus.


Pssm-ID: 460630  Cd Length: 134  Bit Score: 195.86  E-value: 5.49e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  26 GGPFSLTTHNGEPKTDKDFLGQWVLIYFGFTHCPDICPEELEKMIEVVEEIDsiPSLPNLTPLFITIDPERDTKEAIATY 105
Cdd:pfam02630   1 GGPFELVDQDGKAVTEADFEGRPSLVFFGFTHCPDVCPTTLPNMAQVLDALG--EEGIDVQPVFITVDPERDTPEVLAEY 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958660239 106 VKEFSPKLVGLTGTKEEIDGVARAYRVYYSPGPkDEDEDYIVDHTIIMYLIGPDGEF 162
Cdd:pfam02630  79 LEAFGPRIIGLTGSPEQIAAAARAFRVYYEKVP-DDGGDYTVDHTASVYLVDPDGRF 134
Sco1 COG1999
Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, ...
 30-185 8.05e-53

Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441602  Cd Length: 156  Bit Score: 165.84  E-value: 8.05e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  30 SLTTHNGEPKTDKDFLGQWVLIYFGFTHCPDICPEELEKMIEVVEEIDSIPSlPNLTPLFITIDPERDTKEAIATYVKEF 109
Cdd:COG1999     4 TLTDQDGKPVTLADLRGKPVLVFFGYTSCPDVCPTTLANLAQVQEALGEDGG-DDVQVLFISVDPERDTPEVLKAYAEAF 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958660239 110 S-PKLVGLTGTKEEIDGVARAYRVYYSpgpKDEDEDYIVDHTIIMYLIGPDGEFLDYFGQNKKKAEIAGSIAAHMRS 185
Cdd:COG1999    83 GaPRWIGLTGDPEEIAALAKAFGVYYE---KVPDGDYTFDHSAAVYLVDPDGRLRGYYPAGEDPEELAADLKALLEE 156
Bcp COG1225
Peroxiredoxin [Posttranslational modification, protein turnover, chaperones];
29-161 8.44e-11

Peroxiredoxin [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440838 [Multi-domain]  Cd Length: 136  Bit Score: 57.18  E-value: 8.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  29 FSLTTHNGEPKTDKDFLGQWVLIYFGFTHCPdICPEELEKMIEVVEEIDSipslPNLTPLFITIDPERDTKEAIATYVKE 108
Cdd:COG1225     4 FTLPDLDGKTVSLSDLRGKPVVLYFYATWCP-GCTAELPELRDLYEEFKD----KGVEVLGVSSDSDEAHKKFAEKYGLP 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958660239 109 FsPKLVGLTGTkeeidgVARAYRVYYSPGpkdededyivdhtiiMYLIGPDGE 161
Cdd:COG1225    79 F-PLLSDPDGE------VAKAYGVRGTPT---------------TFLIDPDGK 109
TrxA COG0526
Thiol-disulfide isomerase or thioredoxin [Posttranslational modification, protein turnover, ...
 18-161 4.62e-10

Thiol-disulfide isomerase or thioredoxin [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440292 [Multi-domain]  Cd Length: 139  Bit Score: 55.08  E-value: 4.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  18 RSIGKPLLggPFSLTTHNGEPKTDKDFLGQWVLIYFGFTHCPDiCPEELEKMIEVVEEIDSIPslpnltplFITIDPErD 97
Cdd:COG0526     2 KAVGKPAP--DFTLTDLDGKPLSLADLKGKPVLVNFWATWCPP-CRAEMPVLKELAEEYGGVV--------FVGVDVD-E 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958660239  98 TKEAIATYVKEFSPKLVGLTGTKEEidgVARAYRVYYSPgpkdededyivdHTiimYLIGPDGE 161
Cdd:COG0526    70 NPEAVKAFLKELGLPYPVLLDPDGE---LAKAYGVRGIP------------TT---VLIDKDGK 115
AhpC-TSA pfam00578
AhpC/TSA family; This family contains proteins related to alkyl hydroperoxide reductase (AhpC) ...
 29-148 3.07e-09

AhpC/TSA family; This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA).


Pssm-ID: 425763 [Multi-domain]  Cd Length: 124  Bit Score: 52.61  E-value: 3.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  29 FSLTTHNGEPKTDKDFLGQWVLIYF-GFTHCPdICPEELEKMIEVVEEIDSIpslpNLTPLFITIDPERDTKEAIATYVK 107
Cdd:pfam00578   8 FELPDGDGGTVSLSDYRGKWVVLFFyPADWTP-VCTTELPALADLYEEFKKL----GVEVLGVSVDSPESHKAFAEKYGL 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1958660239 108 EFsPKLVGLTGTkeeidgVARAYRVYYSPGPKDEDEDYIVD 148
Cdd:pfam00578  83 PF-PLLSDPDGE------VARAYGVLNEEEGGALRATFVID 116
TlpA_like_family cd02966
TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are ...
 28-161 3.24e-07

TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.


Pssm-ID: 239264 [Multi-domain]  Cd Length: 116  Bit Score: 46.85  E-value: 3.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660239  28 PFSLTTHNGEPKTDKDFLGQWVLIYFGFTHCPdICPEELEKMIEVVEEIDSipslPNLTplFITIDPERDTKEAIATYVK 107
Cdd:cd02966     1 DFSLPDLDGKPVSLSDLKGKVVLVNFWASWCP-PCRAEMPELEALAKEYKD----DGVE--VVGVNVDDDDPAAVKAFLK 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958660239 108 EFSPKLVGLTGTKEEidgVARAYRVYYSPgpkdededyivdhtiIMYLIGPDGE 161
Cdd:cd02966    74 KYGITFPVLLDPDGE---LAKAYGVRGLP---------------TTFLIDRDGR 109
PRX_family cd02971
Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins ...
 29-75 8.35e-03

Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a cysteine sulfenic acid intermediate. The second step of the reaction, the resolution of the intermediate, distinguishes the different types of PRXs. The presence or absence of a second cysteine (the resolving cysteine) classifies PRXs as either belonging to the 2-cys or 1-cys type. The resolving cysteine of 2-cys PRXs is either on the same chain (atypical) or on the second chain (typical) of a functional homodimer. Structural and motif analysis of this growing family supports the need for a new classification system. The peroxidase activity of PRXs is regulated in vivo by irreversible cysteine over-oxidation into a sulfinic acid, phosphorylation and limited proteolysis.


Pssm-ID: 239269 [Multi-domain]  Cd Length: 140  Bit Score: 35.22  E-value: 8.35e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958660239  29 FSLTTHNGEPKTDKDFLGQWVLIYF---GFThcPdICPEELEKMIEVVEE 75
Cdd:cd02971     5 FTLPATDGGEVSLSDFKGKWVVLFFypkDFT--P-VCTTELCAFRDLAEE 51
 
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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