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a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [ 81649]
Superfamily:   a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [ 81648]
Families:   a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [ 81647] (2)


Superfamily statistics
Genomes (1,220) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,585 95,418 8
Proteins 1,534 95,273 8


Functional annotation
General category Metabolism
Detailed category Energy

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 0.0429 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.8766 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.0687 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.05879 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.04091 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.003939 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.01104 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0.0000000009206 Moderately Informative Direct
Biological Process (BP) generation of precursor metabolites and energy 0.00000006905 Moderately Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0.000001121 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000001829 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000006712 Moderately Informative Direct
Biological Process (BP) glycosyl compound metabolic process 0.00004037 Moderately Informative Direct
Biological Process (BP) electron transport chain 0.000000000009048 Informative Direct
Biological Process (BP) cellular respiration 0.000000001012 Informative Direct
Biological Process (BP) ATP metabolic process 0.00000002973 Informative Direct
Biological Process (BP) phosphorylation 0.000184 Informative Direct
Molecular Function (MF) oxidoreductase activity 0.00000000003374 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.0000000001633 Moderately Informative Direct
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0 Informative Direct
Cellular Component (CC) protein complex 0.000001731 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.003242 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2384 Least Informative Inherited
Cellular Component (CC) membrane 0.00976 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.02555 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0000001165 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.0000001553 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.00000016 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0.000001066 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.000002046 Moderately Informative Direct
Cellular Component (CC) cytochrome complex 0.0000000000009312 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.000000000002192 Informative Direct
Cellular Component (CC) respiratory chain complex 0.000000000002901 Informative Direct
Cellular Component (CC) transporter complex 0.00000001564 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.0001409 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0002364 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain complex III 0.00000000001373 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
Coding sequence diversityRNA editing0.00002462Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Molecular functionUbiquinone0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR005798 SSF81648 Protein matches
Abstract

In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III - also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a analogous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase , also known as the b6f complex.

Cytochrome b/b6 [PubMed2509716, PubMed8329437] is an integral membrane protein of approximately 400 amino acid residues that probably has 8 transmembrane segments. In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. The sequence of petB is colinear with the N-terminal part of mitochondrial cytochrome b, while petD corresponds to the C-terminal part. Cytochrome b/b6 non-covalently binds two heme groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two heme groups.

Apart from regions around some of the histidine heme ligands, there are a few conserved regions in the sequence of b/b6. The best conserved of these regions includes an invariant P-E-W triplet which lies in the loop that separates the fifth and sixth transmembrane segments. It seems to be important for electron transfer at the ubiquinone redox site - called Qz or Qo (where o stands for outside) - located on the outer side of the membrane. This entry is the C-terminus of these proteins.


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) · 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 a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 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 a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 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) · UniProtKB KeyWords (KW) · Internal database links ]