SUPERFAMILY 1.75 HMM library and genome assignments server

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Fe-only hydrogenase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Fe-only hydrogenase [ 53919]
Superfamily:   Fe-only hydrogenase [ 53920]
Families:   Fe-only hydrogenase [ 53921] (2)


Superfamily statistics
Genomes (765) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 1,562 11,839 3
Proteins 1,540 11,794 3


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donors0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR009016 SSF53920 Protein matches
Abstract

The iron-only hydrogenases catalyse the two-electron reduction of two protons to yield dihydrogen, as part of an energy cycle. Fe-only hydrogenases are restricted to strictly anaerobic microbes, and are often very sensitive to molecular oxygen. The cytoplasmic monomeric Fe hydrogenases are involved in hydrogen production, while the periplasmic, heterodimeric Fe hydrogenases are involved in hydrogen uptake. Fe hydrogenases consist of two, intertwined domains, the catalytic domain [PubMed9836629] and the larger subunit C domain [PubMed10368269]. The larger subunit C domain can be divided into three subdomains. There are five distinct metal clusters, one in the catalytic domain. This entry represents the two intertwined domains, the catalytic domain and the large subunit C domain.


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) ]

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 2 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 Fe-only hydrogenase 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 2 hidden Markov models representing the Fe-only hydrogenase 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) · Internal database links ]