SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (500) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 2,739 16,799 7
Proteins 2,673 16,338 7


Functional annotation
General category Metabolism
Detailed category Redox

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)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)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)abnormal iris morphology0Highly InformativeDirect
Mammalian Phenotype (MP)abnormal coat/hair pigmentation0Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.009658Least InformativeInherited
Worm Phenotype (WP)germ cell ionizing radiation response variant0.000000007994Highly InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus DEvelopment stage (XDE)post-embryonic stage0Least 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)Isomerases0.2005Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.002693InformativeInherited
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 donors0.000000000000009252Highly InformativeDirect
Enzyme Commission (EC)Transposing C=C bonds0.00000004429Highly InformativeDirect

Document: EC 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]