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 2017_06 genome PDB chains (SCOP 1.75)
Domains 2,739 14,788 7
Proteins 2,673 14,336 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) cellular aromatic compound metabolic process 0.00005875 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00009284 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0002024 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0003722 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.109 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.9989 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6437 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.00000000003377 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.00000000007429 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0000000007538 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.8576 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.5047 Moderately Informative Inherited
Biological Process (BP) pigment metabolic process 0 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0 Informative Direct
Biological Process (BP) secondary metabolic process 0 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.0000001042 Informative Direct
Biological Process (BP) phenol-containing compound metabolic process 0 Highly Informative Direct
Biological Process (BP) pigmentation 0.000000000000001925 Highly Informative Direct
Biological Process (BP) secondary metabolite biosynthetic process 0.00000000000001079 Highly Informative Direct
Biological Process (BP) vesicle organization 0.000000002564 Highly Informative Direct
Molecular Function (MF) binding 0.02699 Least Informative Inherited
Molecular Function (MF) metal ion binding 0 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 0.00000000000002862 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.0001636 Moderately Informative Direct
Molecular Function (MF) anion binding 0.01339 Moderately Informative Inherited
Molecular Function (MF) intramolecular oxidoreductase activity 0.00000004064 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0002753 Informative Direct
Molecular Function (MF) identical protein binding 0.0008782 Informative Direct
Molecular Function (MF) copper ion binding 0 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0.0000000000007525 Highly Informative Direct
Molecular Function (MF) monooxygenase activity 0.000000005345 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.0000001266 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.00001394 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0000551 Highly Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.747 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) vesicle 0.000000002375 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.00231 Moderately Informative Inherited
Cellular Component (CC) whole membrane 0.002395 Moderately Informative Inherited
Cellular Component (CC) cytoplasmic vesicle part 0.0000342 Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.0000001967 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 bonds0.000000005689InformativeDirect
Enzyme Commission (EC)Monophenol monooxygenase0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.0000001298Least InformativeDirect
Biological processOxygen transport0Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentPlastid0.0000161Moderately InformativeDirect
Cellular componentThylakoid0.00000000185InformativeDirect
Cellular componentChloroplast0.000001365InformativeDirect
DiseaseAlbinism0Highly InformativeDirect
DomainSignal0.00000000000000185Least InformativeDirect
DomainTransit peptide0.0005509Moderately 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 bond0.00003452Least 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]