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Di-copper centre-containing domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Di-copper centre-containing domain [ 48055]
Superfamily:   Di-copper centre-containing domain [ 48056] (2)
Families:   Hemocyanin middle domain [ 48057] (2)
  Catechol oxidase [ 48061]

 Superfamily statistics
Genomes (403) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,352 5,940 7
Proteins 2,313 5,748 7

 Functional annotation
General category Metabolism
Detailed category Redox

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 1.621e-08 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1.019e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 4.79e-07 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0004539 Least Informative Direct
Biological Process (BP) developmental process 0.5083 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.6852 Least Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 5.753e-08 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 4.768e-07 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 1.936e-05 Moderately Informative Direct
Biological Process (BP) organelle organization 0.6092 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2629 Moderately Informative Inherited
Biological Process (BP) organ development 0.4243 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) pigment metabolic process 0 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 4.008e-15 Informative Direct
Biological Process (BP) cell proliferation 2.985e-05 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.002741 Informative Inherited
Biological Process (BP) phenol-containing compound metabolic process 0 Highly Informative Direct
Biological Process (BP) pigment biosynthetic process 0 Highly Informative Direct
Biological Process (BP) secondary metabolite biosynthetic process 3.514e-12 Highly Informative Direct
Biological Process (BP) vesicle organization 1.331e-08 Highly Informative Direct
Molecular Function (MF) binding 0.001666 Least Informative Inherited
Molecular Function (MF) cation binding 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 1.523e-07 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 2.794e-05 Moderately Informative Direct
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.00563 Moderately Informative Inherited
Molecular Function (MF) transition metal ion binding 0 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 6.171e-12 Informative Direct
Molecular Function (MF) protein dimerization activity 0.001323 Informative Inherited
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0 Highly Informative Direct
Molecular Function (MF) copper ion binding 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 8.444e-07 Highly Informative Direct
Molecular Function (MF) monooxygenase activity 1.525e-06 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 2.056e-05 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.0001263 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.6423 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) vesicle 2.749e-09 Moderately Informative Direct
Cellular Component (CC) extracellular region 6.634e-08 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.02012 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.1473 Moderately Informative Inherited
Cellular Component (CC) vesicle membrane 1.735e-05 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 2.366e-05 Highly Informative Direct

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)Isomerases0.1491Least InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.001764Moderately InformativeInherited
Enzyme Commission (EC)Transposing C==C bonds5.689e-09InformativeDirect
Enzyme Commission (EC)Monophenol monooxygenase0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)immune system disease0Least InformativeDirect
Disease Ontology (DO)cell type cancer0Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease0Moderately InformativeDirect
Disease Ontology (DO)vitiligo0Highly InformativeDirect
Disease Ontology (DO)melanoma0Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal eye morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)integument phenotype0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal coat appearance0InformativeDirect
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0InformativeDirect
Mammalian Phenotype (MP)abnormal uvea morphology0InformativeDirect
Mammalian Phenotype (MP)abnormal iris morphology0Highly InformativeDirect
Mammalian Phenotype (MP)abnormal coat/hair pigmentation0Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)electrophoretic variant6.843e-07InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect

Document: XA 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)Isomerases0.1885Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.002589InformativeInherited
Enzyme Commission (EC)With another compound as one donor, and incorporation of one atom of oxygen0Highly InformativeDirect
Enzyme Commission (EC)Acting on diphenols and related substances as donors6.488e-14Highly InformativeDirect
Enzyme Commission (EC)Transposing C==C bonds3.758e-08Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport4.138e-08Least InformativeDirect
Biological processOxygen transport0Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentPlastid1.198e-05Moderately InformativeDirect
Cellular componentThylakoid1.433e-09InformativeDirect
Cellular componentChloroplast6.455e-07Highly InformativeDirect
DiseaseAlbinism0Highly InformativeDirect
DomainSignal2.941e-14Least InformativeDirect
DomainTransit peptide0.0005945Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionCopper0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMonooxygenase0Highly InformativeDirect
Post-translational modificationStorage protein0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond3.731e-05Least InformativeDirect
Post-translational modificationThioether bond0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)pigment biosynthesis0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR008922 SSF48056 Protein matches
Abstract

Copper active sites play a major role in biological dioxygen activation. Oxygen intermediates have been studied in detail for the proteins and enzymes involved in reversible O(2) binding (hemocyanin), activation (tyrosinase), and four-electron reduction to water (multicopper oxidases). Tyrosinase binds two copper ions (CuA and CuB). Each of the two copper ions has been shown to be bound by three conserved histidines residues. The regions around these copper-binding ligands are well-conserved and also shared by some hemocyanins, which are copper-containing oxygen carriers from the hemolymph of many molluscs and arthropods [PubMed12404359].


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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 5 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 Di-copper centre-containing domain 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 5 hidden Markov models representing the Di-copper centre-containing domain 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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.