SUPERFAMILY 1.75 HMM library and genome assignments server


Fe,Mn superoxide dismutase (SOD), C-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Fe,Mn superoxide dismutase (SOD), C-terminal domain [ 54718]
Superfamily:   Fe,Mn superoxide dismutase (SOD), C-terminal domain [ 54719]
Families:   Fe,Mn superoxide dismutase (SOD), C-terminal domain [ 54720] (3)


Superfamily statistics
Genomes (2,753) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,496 0 53
Proteins 4,489 0 53


Functional annotation
General category Metabolism
Detailed category Redox

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

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GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of metabolic process 0.0004954 Least Informative Direct
Biological Process (BP) developmental process 0.0002861 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0002342 Least Informative Direct
Biological Process (BP) response to stimulus 9.067e-15 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.05375 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1774 Least Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.0003973 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 5.095e-06 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 4.818e-06 Moderately Informative Direct
Biological Process (BP) cellular response to stress 5.795e-13 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 6.028e-07 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 8.438e-11 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 1.534e-13 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0.1187 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.4252 Moderately Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 5.819e-05 Informative Direct
Biological Process (BP) response to oxidative stress 0 Informative Direct
Biological Process (BP) mitochondrion organization 2.165e-07 Informative Direct
Biological Process (BP) response to inorganic substance 0 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 4.285e-13 Informative Direct
Biological Process (BP) response to superoxide 0 Highly Informative Direct
Biological Process (BP) superoxide metabolic process 0 Highly Informative Direct
Biological Process (BP) aging 0 Highly Informative Direct
Biological Process (BP) cellular response to reactive oxygen species 0 Highly Informative Direct
Molecular Function (MF) binding 0.01152 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0 Moderately Informative Direct
Molecular Function (MF) transition metal ion binding 0 Informative Direct
Molecular Function (MF) antioxidant activity 0 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 2.698e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0139 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01123 Least Informative Inherited
Cellular Component (CC) membrane 0.9243 Least Informative Inherited
Cellular Component (CC) mitochondrial part 3.486e-11 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.002603 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2611 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.05705 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 6.138e-08 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

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EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Superoxide dismutase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

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YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least 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 superoxide as acceptor1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processStress response0.0001331InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationAcetylation0.0005518Least InformativeDirect
Post-translational modificationNitration0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001189 SSF54719 Protein matches
Abstract

Superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [PubMed3315461, PubMed3345848, PubMed1556751]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers.

The structure of Fe/MnSODs can be divided into two domains, an alpha N-terminal domain and an alpha/beta C-terminal domain, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist [PubMed9537987]. The structure of the C-terminal domain is of the alpha/beta type, and consists of a three-stranded antiparallel beta-sheet in the order 213, along with four helices in the arrangement alpha/beta(2)/alpha/beta/alpha(2) [PubMed9931259].


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) · Enzyme Commission (EC) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 20 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,Mn superoxide dismutase (SOD), C-terminal 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 20 hidden Markov models representing the Fe,Mn superoxide dismutase (SOD), C-terminal 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]