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Conserved domains on  [gi|1337428515|ref|WP_103272017|]
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SCO family protein [Achromobacter sp. AONIH1]

Protein Classification

SCO family protein( domain architecture ID 10005092)

SCO (Synthesis of Cytochrome c Oxidase) family protein is required for the proper assembly of cytochrome c oxidase

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sco1 COG1999
Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, ...
 49-200 6.77e-67

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


:

Pssm-ID: 441602  Cd Length: 156  Bit Score: 202.05  E-value: 6.77e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPDVCPTSLAELAEAMKKLGADA-DRVQVLLITVDPERDTPDILKQYVTAFD 127
Cdd:COG1999     4 TLTDQDGKPVTLADLRGKPVLVFFGYTSCPDVCPTTLANLAQVQEALGEDGgDDVQVLFISVDPERDTPEVLKAYAEAFG 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1337428515 128 -PRFLGLTGTPDQVKKAAASFKAYYAKAPtkDGGYSMDHTAAFYLLDGKGESRVLANNNIGVDALVHDIQALLK 200
Cdd:COG1999    84 aPRWIGLTGDPEEIAALAKAFGVYYEKVP--DGDYTFDHSAAVYLVDPDGRLRGYYPAGEDPEELAADLKALLE 155
 
Name Accession Description Interval E-value
Sco1 COG1999
Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, ...
 49-200 6.77e-67

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


Pssm-ID: 441602  Cd Length: 156  Bit Score: 202.05  E-value: 6.77e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPDVCPTSLAELAEAMKKLGADA-DRVQVLLITVDPERDTPDILKQYVTAFD 127
Cdd:COG1999     4 TLTDQDGKPVTLADLRGKPVLVFFGYTSCPDVCPTTLANLAQVQEALGEDGgDDVQVLFISVDPERDTPEVLKAYAEAFG 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1337428515 128 -PRFLGLTGTPDQVKKAAASFKAYYAKAPtkDGGYSMDHTAAFYLLDGKGESRVLANNNIGVDALVHDIQALLK 200
Cdd:COG1999    84 aPRWIGLTGDPEEIAALAKAFGVYYEKVP--DGDYTFDHSAAVYLVDPDGRLRGYYPAGEDPEELAADLKALLE 155
SCO1-SenC pfam02630
SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. ...
 49-177 1.20e-66

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: 200.48  E-value: 1.20e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPDVCPTSLAELAEAMKKLGADADRVQVLLITVDPERDTPDILKQYVTAFDP 128
Cdd:pfam02630   5 ELVDQDGKAVTEADFEGRPSLVFFGFTHCPDVCPTTLPNMAQVLDALGEEGIDVQPVFITVDPERDTPEVLAEYLEAFGP 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1337428515 129 RFLGLTGTPDQVKKAAASFKAYYAKAPTKDGGYSMDHTAAFYLLDGKGE 177
Cdd:pfam02630  85 RIIGLTGSPEQIAAAARAFRVYYEKVPDDGGDYTVDHTASVYLVDPDGR 133
SCO cd02968
SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to ...
 49-177 5.05e-63

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: 191.66  E-value: 5.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPDVCPTSLAELAEAMKKLGADA-DRVQVLLITVDPERDTPDILKQYVTAFD 127
Cdd:cd02968     6 TLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGgDDVQVVFISVDPERDTPEVLKAYAKAFG 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1337428515 128 PRFLGLTGTPDQVKKAAASFKAYYAKAPTKDGGYSMDHTAAFYLLDGKGE 177
Cdd:cd02968    86 PGWIGLTGTPEEIEALAKAFGVYYEKVPEDDGDYLVDHSAAIYLVDPDGK 135
 
Name Accession Description Interval E-value
Sco1 COG1999
Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, ...
 49-200 6.77e-67

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


Pssm-ID: 441602  Cd Length: 156  Bit Score: 202.05  E-value: 6.77e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPDVCPTSLAELAEAMKKLGADA-DRVQVLLITVDPERDTPDILKQYVTAFD 127
Cdd:COG1999     4 TLTDQDGKPVTLADLRGKPVLVFFGYTSCPDVCPTTLANLAQVQEALGEDGgDDVQVLFISVDPERDTPEVLKAYAEAFG 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1337428515 128 -PRFLGLTGTPDQVKKAAASFKAYYAKAPtkDGGYSMDHTAAFYLLDGKGESRVLANNNIGVDALVHDIQALLK 200
Cdd:COG1999    84 aPRWIGLTGDPEEIAALAKAFGVYYEKVP--DGDYTFDHSAAVYLVDPDGRLRGYYPAGEDPEELAADLKALLE 155
SCO1-SenC pfam02630
SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. ...
 49-177 1.20e-66

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: 200.48  E-value: 1.20e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPDVCPTSLAELAEAMKKLGADADRVQVLLITVDPERDTPDILKQYVTAFDP 128
Cdd:pfam02630   5 ELVDQDGKAVTEADFEGRPSLVFFGFTHCPDVCPTTLPNMAQVLDALGEEGIDVQPVFITVDPERDTPEVLAEYLEAFGP 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1337428515 129 RFLGLTGTPDQVKKAAASFKAYYAKAPTKDGGYSMDHTAAFYLLDGKGE 177
Cdd:pfam02630  85 RIIGLTGSPEQIAAAARAFRVYYEKVPDDGGDYTVDHTASVYLVDPDGR 133
SCO cd02968
SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to ...
 49-177 5.05e-63

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: 191.66  E-value: 5.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPDVCPTSLAELAEAMKKLGADA-DRVQVLLITVDPERDTPDILKQYVTAFD 127
Cdd:cd02968     6 TLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGgDDVQVVFISVDPERDTPEVLKAYAKAFG 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1337428515 128 PRFLGLTGTPDQVKKAAASFKAYYAKAPTKDGGYSMDHTAAFYLLDGKGE 177
Cdd:cd02968    86 PGWIGLTGTPEEIEALAKAFGVYYEKVPEDDGDYLVDHSAAIYLVDPDGK 135
TrxA COG0526
Thiol-disulfide isomerase or thioredoxin [Posttranslational modification, protein turnover, ...
 48-201 3.70e-09

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


Pssm-ID: 440292 [Multi-domain]  Cd Length: 139  Bit Score: 53.16  E-value: 3.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  48 MELVDYNGKTRKLSDFSGKVVVAFFGFTQCPDvCPTSLAELAEAMKKLGadadRVQVLLITVDperDTPDILKQYVTAFD 127
Cdd:COG0526    11 FTLTDLDGKPLSLADLKGKPVLVNFWATWCPP-CRAEMPVLKELAEEYG----GVVFVGVDVD---ENPEAVKAFLKELG 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1337428515 128 PRFLGLTgtpDQVKKAAASFKAYYakAPTkdggysmdhtaaFYLLDGKGESRVLANNNIGVDALVHDIQALLKG 201
Cdd:COG0526    83 LPYPVLL---DPDGELAKAYGVRG--IPT------------TVLIDKDGKIVARHVGPLSPEELEEALEKLLAK 139
AhpC-TSA pfam00578
AhpC/TSA family; This family contains proteins related to alkyl hydroperoxide reductase (AhpC) ...
 28-112 5.54e-08

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: 49.53  E-value: 5.54e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  28 GESAPQFkgsdisgtrlgqgmELVDYNGKTRKLSDFSGK-VVVAFFGFTQCPdVCPTSLAELAEAMKKLGADAdrVQVLL 106
Cdd:pfam00578   2 GDKAPDF--------------ELPDGDGGTVSLSDYRGKwVVLFFYPADWTP-VCTTELPALADLYEEFKKLG--VEVLG 64


                  ....*.
gi 1337428515 107 ITVDPE 112
Cdd:pfam00578  65 VSVDSP 70
Bcp COG1225
Peroxiredoxin [Posttranslational modification, protein turnover, chaperones];
49-112 6.75e-08

Peroxiredoxin [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440838 [Multi-domain]  Cd Length: 136  Bit Score: 49.48  E-value: 6.75e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPdVCPTSLAELAEAMKKLGadADRVQVLLITVDPE 112
Cdd:COG1225     5 TLPDLDGKTVSLSDLRGKPVVLYFYATWCP-GCTAELPELRDLYEEFK--DKGVEVLGVSSDSD 65
PRX_AhpE_like cd03018
Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium ...
 28-111 1.26e-07

Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective 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 thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.


Pssm-ID: 239316 [Multi-domain]  Cd Length: 149  Bit Score: 48.81  E-value: 1.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  28 GESAPQFkgsdisgtrlgqgmELVDYNGKTRKLSDFSG--KVVVAFFGFTQCPdVCPTSLAELAEAMKKLgaDADRVQVL 105
Cdd:cd03018     4 GDKAPDF--------------ELPDQNGQEVRLSEFRGrkPVVLVFFPLAFTP-VCTKELCALRDSLELF--EAAGAEVL 66


                  ....*.
gi 1337428515 106 LITVDP 111
Cdd:cd03018    67 GISVDS 72
TlpA_like_family cd02966
TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are ...
 49-179 5.54e-06

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: 43.76  E-value: 5.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  49 ELVDYNGKTRKLSDFSGKVVVAFFGFTQCPdVCPTSLAELAEAMKKLGadADRVQVLLITVDpeRDTPDILKQYVTAFDP 128
Cdd:cd02966     3 SLPDLDGKPVSLSDLKGKVVLVNFWASWCP-PCRAEMPELEALAKEYK--DDGVEVVGVNVD--DDDPAAVKAFLKKYGI 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1337428515 129 RFLGLTgtpDQVKKAAASFKAYYakAPTkdggysmdhtaaFYLLDGKGESR 179
Cdd:cd02966    78 TFPVLL---DPDGELAKAYGVRG--LPT------------TFLIDRDGRIR 111
PRX_Typ2cys cd03015
Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant ...
 56-110 1.01e-04

Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric interface in atypical 2-cys PRX and PRX5) at the opposite end of the monomer to form the stable decameric (pentamer of dimers) structure.


Pssm-ID: 239313  Cd Length: 173  Bit Score: 41.34  E-value: 1.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1337428515  56 KTRKLSDFSGKVVVAFF---GFTQcpdVCPTSLAELAEAMKKLgadADR-VQVLLITVD 110
Cdd:cd03015    20 KEISLSDYKGKWVVLFFyplDFTF---VCPTEIIAFSDRYEEF---KKLnAEVLGVSTD 72
PRX_like1 cd02969
Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. ...
 28-130 1.41e-03

Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs 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 thioredoxin, glutathione, trypanothione and AhpF.


Pssm-ID: 239267 [Multi-domain]  Cd Length: 171  Bit Score: 37.99  E-value: 1.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1337428515  28 GESAPQFkgsdisgtrlgqgmELVDYNGKTRKLSDFSGK--VVVAFFgftqCPDvCPTSLAeLAEAMKKLGAD--ADRVQ 103
Cdd:cd02969     1 GSPAPDF--------------SLPDTDGKTYSLADFADGkaLVVMFI----CNH-CPYVKA-IEDRLNRLAKEygAKGVA 60

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1337428515 104 VLLI----TVDPERDTPDILKQYVTAFDPRF 130
Cdd:cd02969    61 VVAInsndIEAYPEDSPENMKAKAKEHGYPF 91
 
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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