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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 (1,224) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1,591 138,674 8
Proteins 1,540 138,337 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) organonitrogen compound metabolic process 0.2332 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.06338 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.07308 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7869 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.04357 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.04585 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.004945 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0.000000001184 Moderately Informative Direct
Biological Process (BP) generation of precursor metabolites and energy 0.00000008865 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000002104 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000008353 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0002797 Moderately Informative Direct
Biological Process (BP) electron transport chain 0.000000000009037 Informative Direct
Biological Process (BP) cellular respiration 0.00000000104 Informative Direct
Biological Process (BP) ATP metabolic process 0.0000000348 Informative Direct
Biological Process (BP) phosphorylation 0.0001949 Informative Direct
Molecular Function (MF) oxidoreductase activity 0.00000000004616 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.000000000241 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 0.000002566 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.1789 Least Informative Inherited
Cellular Component (CC) membrane 0.004572 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.001867 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.02946 Least Informative Inherited
Cellular Component (CC) mitochondrial envelope 0.0000000001363 Moderately Informative Direct
Cellular Component (CC) organelle inner membrane 0.0000000003207 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.0000002721 Moderately Informative Direct
Cellular Component (CC) mitochondrial protein complex 0.000001163 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0.00003816 Moderately Informative Direct
Cellular Component (CC) cytochrome complex 0.0000000000006614 Informative Direct
Cellular Component (CC) respiratory chain complex 0.000000000003532 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.000000000004054 Informative Direct
Cellular Component (CC) transporter complex 0.00000002327 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.0001473 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0003402 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain complex III 0.0000009789 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 editing0.00002375Moderately 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

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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 ]