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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 (1,223) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1,588 138,674 8
Proteins 1,537 138,337 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) cellular nitrogen compound metabolic process 0.08131 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.00594 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.05135 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.04873 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.2504 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7946 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.07059 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0.000000001514 Moderately Informative Direct
Biological Process (BP) generation of precursor metabolites and energy 0.0000001085 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000002499 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000009884 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0003086 Moderately Informative Direct
Biological Process (BP) electron transport chain 0.00000000001185 Informative Direct
Biological Process (BP) cellular respiration 0.000000001353 Informative Direct
Biological Process (BP) ATP metabolic process 0.00000004372 Informative Direct
Biological Process (BP) phosphorylation 0.0002187 Informative Direct
Molecular Function (MF) oxidoreductase activity 0.00000000006437 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.0000000002843 Moderately Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) electron carrier activity 0 Informative Direct
Cellular Component (CC) macromolecular complex 0.000357 Least Informative Direct
Cellular Component (CC) membrane 0.004981 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0321 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.002127 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1806 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.000000255 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.0000003061 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.0000004004 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0.00003606 Moderately Informative Direct
Cellular Component (CC) cytochrome complex 0.0000000000007487 Informative Direct
Cellular Component (CC) respiratory chain complex 0.000000000003908 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.00000000000396 Informative Direct
Cellular Component (CC) transporter complex 0.00000002227 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.0001274 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0002322 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain complex III 0.0000009448 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 processPhotosynthesis0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
Coding sequence diversityRNA editing0.00002408Moderately 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 ]