SUPERFAMILY 1.75 HMM library and genome assignments server


Nickel-containing superoxide dismutase, NiSOD superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Four-helical up-and-down bundle [ 47161] (28)
Superfamily:   Nickel-containing superoxide dismutase, NiSOD [ 109770]
Families:   Nickel-containing superoxide dismutase, NiSOD [ 109771]


Superfamily statistics
Genomes (109) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 114 242 3
Proteins 114 242 3


Functional annotation
General category coiled coil
Detailed category This is a complex coiled arrangement. The details of which will appear on this page shortly (some coiled coil details are being checked before they are included on the site). If you want to see examples of the states please click here here. If you require further details urgently please contact Owen Rackham

Document:
Function annotation of SCOP domain superfamilies

InterPro annotation
Cross references IPR014123 SSF109770 Protein matches
Abstract

This entry represents nickel-dependent superoxide dismutase (NiSOD) , a SOD enzyme that uses nickel, rather than iron, manganese, copper, or zinc. All SOD enzymes catalyse the dismutation of toxic superoxide radical anions to oxygen and hydrogen peroxide in order to protect cells from oxidative damage. The catalytic cycle of NiSOD consists of two half-reactions, each initiated by the successive approach of substrate to the metal centre. The first (reductive) phase involves Ni(III) reduction to Ni(II), and the second (oxidative) phase involves the metal reoxidation back to its resting state [PubMed16756300]. NiSOD has a novel SOD fold and assembly, consisting of a hexameric assembly of 4-helix bundles of up-and-down topology, which contains a 9-residue nickel-hook structural motif that is critical for metal binding and catalysis [PubMed15209499]. A gene for a required protease (NiSOD maturation protease) is adjacent to the NiSOD gene.


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 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 Nickel-containing superoxide dismutase, NiSOD 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 Nickel-containing superoxide dismutase, NiSOD 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 · Internal database links ]