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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 (495) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,703 8,009 7
Proteins 2,650 7,777 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 0.000001568 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00001673 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00006993 Least Informative Direct
Biological Process (BP) developmental process 0.6785 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.001474 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 0.9617 Least Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.000000004374 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.00000001467 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00000003949 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.000156 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.6728 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.9138 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1991 Moderately Informative Inherited
Biological Process (BP) organ development 0.8164 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0 Informative Direct
Biological Process (BP) secondary metabolic process 0 Informative Direct
Biological Process (BP) pigment metabolic process 0 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.01394 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 0.000000000005214 Highly Informative Direct
Biological Process (BP) vesicle organization 0.00000009299 Highly Informative Direct
Molecular Function (MF) binding 0.2039 Least Informative Inherited
Molecular Function (MF) cation binding 0 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 0.0000003542 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.0000005638 Moderately Informative Direct
Molecular Function (MF) anion binding 0.001544 Moderately Informative Inherited
Molecular Function (MF) intramolecular oxidoreductase activity 0.00000000005252 Informative Direct
Molecular Function (MF) protein dimerization activity 0.00484 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) monooxygenase activity 0.000000001833 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.00000009934 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.000004879 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.0004937 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 0.1555 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) vesicle 0.00000000001283 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.3331 Moderately Informative Inherited
Cellular Component (CC) cytoplasmic vesicle membrane 0.771 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)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 bonds0.000000005689InformativeDirect
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)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)diluted coat color0Highly InformativeDirect
Mammalian Phenotype (MP)abnormal iris morphology0Highly InformativeDirect
Mammalian Phenotype (MP)abnormal eye 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 variant0.000002178InformativeDirect

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)genital system0Least InformativeDirect
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)visual 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)Isomerases0.163Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.002065InformativeInherited
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 donors0.0000000000007704Highly InformativeDirect
Enzyme Commission (EC)Transposing C==C bonds0.00000002853Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.00000004482Least InformativeDirect
Biological processOxygen transport0Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentPlastid0.00001047Moderately InformativeDirect
Cellular componentThylakoid0.000000001042InformativeDirect
Cellular componentChloroplast0.000000701InformativeDirect
DiseaseAlbinism0Highly InformativeDirect
DomainSignal0.000000000000002737Least InformativeDirect
DomainTransit peptide0.0004235Moderately 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 bond0.00003259Least InformativeDirect
Post-translational modificationThioether bond0Highly InformativeDirect

Document: KW 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) ]

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) · Internal database links ]