SUPERFAMILY 1.75 HMM library and genome assignments server

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ISP domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   ISP domain [ 50021]
Superfamily:   ISP domain [ 50022] (3)
Families:   Rieske iron-sulfur protein (ISP) [ 50023] (8)
  Ring hydroxylating alpha subunit ISP domain [ 50033] (6)
  NirD-like [ 158991]


Superfamily statistics
Genomes (2,304) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 11,849 98,890 26
Proteins 11,787 98,701 26


Functional annotation
General category Metabolism
Detailed category E- transfer

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)Acting on paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0000005571InformativeDirect
Enzyme Commission (EC)Nitrite reductase (NAD(P)H)0Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With a reduced iron-sulfur protein as one donor, a0.002936Highly InformativeInherited

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP 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)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0InformativeDirect
Enzyme Commission (EC)Catalysing the translocation of hydrons0InformativeDirect
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors0.06291InformativeInherited
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into one donor0Highly InformativeDirect
Enzyme Commission (EC)With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen0.00000182Highly InformativeDirect
Enzyme Commission (EC)Quinol--cytochrome-c reductase0.00000257Highly InformativeDirect
Enzyme Commission (EC)With another compound as one donor, and incorporation of one atom of oxygen0.000002754Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00001359Highly InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of one atom of oxygen0.4456Highly InformativeInherited

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR005806 SSF50022 Protein matches
Abstract

Ubiquinol-cytochrome c reductase (bc1 complex or complex III) is an enzyme complex of bacterial and mitochondrial oxidative phosphorylation systems It catalyses the oxidoreduction of the mobile redox components ubiquinol and cytochrome c, generating an electrochemical potential, which is linked to ATP synthesis [PubMed2986972, PubMed3004982]. The complex consists of three subunits in most bacteria, and nine in mitochondria: both bacterial and mitochondrial complexes contain cytochrome b and cytochrome c1 subunits, and an iron-sulphur `Rieske' subunit, which contains a high potential 2Fe-2S cluster [PubMed2820981].The mitochondrial form also includes six other subunits that do not possess redox centres. Plastoquinone-plastocyanin reductase (b6f complex), present in cyanobacteria and the chloroplasts of plants, catalyses the oxidoreduction of plastoquinol and cytochrome f. This complex, which is functionally similar to ubiquinol-cytochrome c reductase, comprises cytochrome b6, cytochrome f and Rieske subunits [PubMed1391772].

The Rieske subunit acts by binding either a ubiquinol or plastoquinol anion, transferring an electron to the 2Fe-2S cluster, then releasing the electron to the cytochrome c or cytochrome f haem iron [PubMed2986972, PubMed1391772]. The rieske domain has a [2Fe-2S] centre. Two conserved cysteines that one Fe ion while the other Fe ion is coordinated by two conserved histidines. The 2Fe-2S cluster is bound in the highly conserved C-terminal region of the Rieske subunit.


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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 35 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 ISP 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 35 hidden Markov models representing the ISP 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]