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Cupredoxins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Cupredoxin-like [ 49502] (2)
Superfamily:   Cupredoxins [ 49503] (7)
Families:   Plastocyanin/azurin-like [ 49504] (9)
  Nitrosocyanin [ 63392] (2)
  Periplasmic domain of cytochrome c oxidase subunit II [ 49541] (2)
  Multidomain cupredoxins [ 49550] (7)
  Ephrin ectodomain [ 74874] (2)
  Peptidylarginine deiminase Pad4, N-terminal domain [ 110107]
  SO1698-like [ 141095]


Superfamily statistics
Genomes (2,462) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 37,794 0 222
Proteins 20,799 0 151


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on a heme group of donors0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0Highly InformativeDirect
Enzyme Commission (EC)In linear amidines0.000000000000003021Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)connective tissue disease0.0008688Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.0472Moderately InformativeInherited
Disease Ontology (DO)hemorrhagic disease0.0008001InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.04275Least InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.06402Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.2928Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal uvea morphology0.01108InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.1732InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.03028Least InformativeInherited
Worm Phenotype (WP)apoptosis variant0.0003433Moderately InformativeDirect
Worm Phenotype (WP)cell corpse number decreased0.000000003122Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0.05238Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure0.2853Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.374Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.4537Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.9867Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll1Least InformativeInherited
Plant ANatomical entity (PAN)cotyledon1Moderately InformativeInherited
Plant ANatomical entity (PAN)fruit0.00009594InformativeDirect
Plant ANatomical entity (PAN)rosette leaf0.0003299InformativeDirect
Plant ANatomical entity (PAN)filament0Highly InformativeDirect
Plant ANatomical entity (PAN)leaf epidermis0.0000000000000172Highly InformativeDirect
Plant ANatomical entity (PAN)phyllome vascular system0.00000000003835Highly InformativeDirect
Plant ANatomical entity (PAN)trichome0.000000000191Highly InformativeDirect
Plant ANatomical entity (PAN)embryo sac cell0.005494Highly InformativeInherited
Plant structure DEvelopment stage (PDE)seedling development stage0.000009852InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.1747Moderately InformativeInherited
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors0.00001156InformativeDirect
Enzyme Commission (EC)Acting on diphenols and related substances as donors0Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Acting on a heme group of donors0Highly InformativeDirect
Enzyme Commission (EC)In linear amidines4.978e-16Highly InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0.007262Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processElectron transport0InformativeDirect
Biological processNeurogenesis0.0000000001605InformativeDirect
Biological processHemostasis0.000000001768InformativeDirect
Biological processAngiogenesis0.000003607InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Biological processBlood coagulation0.0000000001244Highly InformativeDirect
Biological processNitrate assimilation0.00000009556Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentSecreted0.000000000000005838Moderately InformativeDirect
Cellular componentPlastid0.1828Moderately InformativeInherited
Cellular componentGPI-anchor0InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
Cellular componentThylakoid0.00000000001895InformativeDirect
Cellular componentChloroplast0.0001997InformativeDirect
Cellular componentApoplast0Highly InformativeDirect
Coding sequence diversityRNA editing0.000005132Moderately InformativeDirect
DiseaseTumor suppressor0.0005343Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionCalcium0.00003124Moderately InformativeDirect
Molecular functionIron1Moderately InformativeInherited
Molecular functionCopper0InformativeDirect
Molecular functionIron transport0.0000000001396Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationSulfation0.000003168InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008972 SSF49503 Protein matches
Abstract

Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as Cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment.

This entry represents cupredoxin proteins, as well as structural homologues to cupredoxin. Structurally, the cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel [PubMed11867755]. Some of these proteins have lost the ability to bind copper. Proteins with a cupredoxin-type fold are found in the following family groups:

  • Mono-domain cupredoxins, such as amicyanin, plastocyanin, pseudoazurin, plantacyanin, azurin, auracyanin, rusticyanin, stellacyanin, and mavicyanin.
  • Multi-domain cupredoxins, such as nitrite reductase (2 domains of this fold), multicopper oxidase CueO, spore coat protein A, ascorbate oxidase (3 domains of this fold), laccase (3 domains of this fold), ceruloplamin (6 domains of this fold), and coagulation factor V.
  • Red copper protein nitrocyanin and the C-terminal of nitrous oxide reductase.
  • Quinol oxidase and the periplasmic domain of cytochrome c oxidase subunit II.
  • Ephrin-a5 and ephrin-b2 ectodomain, which are related to cupredoxins but lack the metal-binding site.
  • The N-terminal domain of protein arginine deiminase Pad4, which is related to cupredoxin but lacks the metal-biding site.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 93 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Cupredoxins domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 93 hidden Markov models representing the Cupredoxins superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]