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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 2017_06 genome PDB chains (SCOP 1.75)
Domains 37,794 209,794 222
Proteins 20,799 148,720 151


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism metabolic process0.8361Least InformativeInherited
Biological Process (BP)response to stimulus0.11171Least InformativeInherited
Biological Process (BP)biological regulation0.82591Least InformativeInherited
Biological Process (BP)oxidation-reduction process0.00015830.0008231Moderately InformativeDirect
Biological Process (BP)single organism signaling0.0089020.885Moderately InformativeInherited
Biological Process (BP)cell communication0.012250.7883Moderately InformativeInherited
Biological Process (BP)cell surface receptor signaling pathway0.000006090.00004296InformativeDirect
Biological Process (BP)response to metal ion0.00039420.0004074InformativeDirect
Biological Process (BP)enzyme linked receptor protein signaling pathway0.000000000080240.00000000000047Highly InformativeDirect
Biological Process (BP)response to copper ion0.00013870.000000002411Highly InformativeDirect
Molecular Function (MF)binding0.053581Least InformativeInherited
Molecular Function (MF)metal ion binding0.000024080.003526Moderately InformativeInherited
Molecular Function (MF)electron carrier activity0.000012420InformativeDirect
Molecular Function (MF)receptor binding0.00034240.00002215InformativeDirect
Molecular Function (MF)copper ion binding7.1e-160Highly InformativeDirect
Cellular Component (CC)membrane0.000019060Least InformativeDirect
Cellular Component (CC)intrinsic component of membrane0.00000049351Moderately InformativeInherited
Cellular Component (CC)anchored component of membrane00Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0.0008231 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.9235 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.885 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.005209 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cell communication 0.7883 Moderately Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0.1232 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.3244 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.4218 Moderately Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.00004296 Informative Direct
Biological Process (BP) response to metal ion 0.0004074 Informative Direct
Biological Process (BP) electron transport chain 0.000000005051 Informative Direct
Biological Process (BP) cellular respiration 0.0002231 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.9606 Informative Inherited
Biological Process (BP) cellular response to inorganic substance 0.009981 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.8162 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.4332 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.7295 Informative Inherited
Biological Process (BP) cation homeostasis 0.07585 Informative Inherited
Biological Process (BP) inorganic ion homeostasis 0.08296 Informative Inherited
Biological Process (BP) generation of neurons 0.4318 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.5654 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.8062 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.1653 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.01557 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.06571 Informative Inherited
Biological Process (BP) response to wounding 0.02872 Informative Inherited
Biological Process (BP) ATP metabolic process 0.002175 Informative Inherited
Biological Process (BP) phosphorylation 0.9539 Informative Inherited
Biological Process (BP) metal ion transport 0.02725 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.00000000000047 Highly Informative Direct
Biological Process (BP) response to copper ion 0.000000002411 Highly Informative Direct
Biological Process (BP) coagulation 0.00000008951 Highly Informative Direct
Biological Process (BP) transition metal ion transport 0.0000006859 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.000007712 Highly Informative Direct
Biological Process (BP) negative regulation of cell development 0.0003143 Highly Informative Direct
Biological Process (BP) negative regulation of nervous system development 0.001789 Highly Informative Inherited
Biological Process (BP) wound healing 0.001839 Highly Informative Inherited
Biological Process (BP) hemostasis 0.01389 Highly Informative Inherited
Biological Process (BP) response to iron ion 0.06582 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.06083 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.001088 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.003526 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) receptor binding 0.00002215 Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.000000004189 Informative Direct
Molecular Function (MF) copper ion binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor 0 Highly Informative Direct
Molecular Function (MF) heme-copper terminal oxidase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) intrinsic component of membrane 1 Moderately Informative Inherited
Cellular Component (CC) respiratory chain complex 0 Informative Direct
Cellular Component (CC) cytochrome complex 0 Informative Direct
Cellular Component (CC) cell surface 0.4329 Informative Inherited
Cellular Component (CC) side of membrane 1 Informative Inherited
Cellular Component (CC) external encapsulating structure 0.07793 Informative Inherited
Cellular Component (CC) anchored component of membrane 0 Highly Informative Direct
Cellular Component (CC) respiratory chain complex IV 0 Highly Informative Direct
Cellular Component (CC) plant-type cell wall 0.000003613 Highly Informative Direct
Cellular Component (CC) symplast 0.000005242 Highly Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.08325 Highly Informative Inherited
Cellular Component (CC) external side of plasma membrane 0.003451 Highly Informative Inherited
Cellular Component (CC) cell-cell junction 0.03444 Highly Informative Inherited

Document: GO annotation of SCOP domains

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processDifferentiation0.0009756Moderately InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processElectron transport0InformativeDirect
Biological processNeurogenesis0.0000000001278InformativeDirect
Biological processHemostasis0.000000001799InformativeDirect
Biological processAngiogenesis0.000003247InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Biological processBlood coagulation0.0000000001231Highly InformativeDirect
Biological processNitrate assimilation0.00000009735Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentSecreted0.000000000000005803Moderately InformativeDirect
Cellular componentPlastid0.1813Moderately InformativeInherited
Cellular componentGPI-anchor0InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
Cellular componentThylakoid0.00000000002013InformativeDirect
Cellular componentChloroplast0.0001807InformativeDirect
Cellular componentApoplast0Highly InformativeDirect
Coding sequence diversityRNA editing0.000005171Moderately InformativeDirect
DiseaseTumor suppressor0.0005297Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionCalcium0.00002609Moderately InformativeDirect
Molecular functionIron1Moderately InformativeInherited
Molecular functionCopper0InformativeDirect
Molecular functionIron transport0.0000000001385Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationSulfation0.00000305InformativeDirect

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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]