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2Fe-2S ferredoxin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   beta-Grasp (ubiquitin-like) [ 54235] (14)
Superfamily:   2Fe-2S ferredoxin-like [ 54292] (2)
Families:   2Fe-2S ferredoxin-related [ 54293] (3)
  2Fe-2S ferredoxin domains from multidomain proteins [ 54312] (13)


Superfamily statistics
Genomes (2,892) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 20,940 121,110 57
Proteins 20,917 121,023 57


Functional annotation
General category Metabolism
Detailed category Redox

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)macromolecule metabolic process0.00088131Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0012690.2182Least InformativeInherited
Biological Process (BP)primary metabolic process0.4611Least InformativeInherited
Molecular Function (MF)binding0.000001440.000873Least InformativeDirect
Molecular Function (MF)metal ion binding0.0000000046580.00000000000002568Moderately InformativeDirect
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)iron ion binding00Highly InformativeDirect
Molecular Function (MF)iron-sulfur cluster binding10Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.00096060.005216Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.083640.000000008318Least InformativeInherited
Cellular Component (CC)plastid00.000000000001503InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000002524 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.2182 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.9506 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4759 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.08266 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000003203 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0002024 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.8271 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.04895 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.8939 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.3561 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.07194 Moderately Informative Inherited
Biological Process (BP) ATP metabolic process 0 Informative Direct
Biological Process (BP) electron transport chain 0 Informative Direct
Biological Process (BP) regulation of hormone levels 0.00001083 Informative Direct
Biological Process (BP) mitochondrion organization 0.00001142 Informative Direct
Biological Process (BP) cellular respiration 0.0001458 Informative Direct
Biological Process (BP) alcohol metabolic process 0.5144 Informative Inherited
Biological Process (BP) phosphorylation 0.5628 Informative Inherited
Biological Process (BP) cell death 0.04403 Informative Inherited
Biological Process (BP) citrate metabolic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) hormone biosynthetic process 0.0000000000008178 Highly Informative Direct
Biological Process (BP) purine-containing compound catabolic process 0.000000001336 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.000004753 Highly Informative Direct
Biological Process (BP) secondary alcohol metabolic process 0.000005226 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0.00001638 Highly Informative Direct
Biological Process (BP) apoptotic process 0.0001431 Highly Informative Direct
Biological Process (BP) aerobic respiration 1 Highly Informative Inherited
Molecular Function (MF) binding 0.000873 Least Informative Direct
Molecular Function (MF) metal ion binding 0.00000000000002568 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.01106 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.000001903 Informative Direct
Molecular Function (MF) identical protein binding 0.00001483 Informative Direct
Molecular Function (MF) coenzyme binding 0.2764 Informative Inherited
Molecular Function (MF) iron ion binding 0 Highly Informative Direct
Molecular Function (MF) iron-sulfur cluster binding 0 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.000000009151 Highly Informative Direct
Molecular Function (MF) NADH dehydrogenase activity 0.00000001931 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.0000003301 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.00001231 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on hydrogen as donor 0.00002273 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000008318 Least Informative Direct
Cellular Component (CC) protein complex 0.0001519 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 0.03348 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.005216 Least Informative Inherited
Cellular Component (CC) organelle inner membrane 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial protein complex 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial envelope 0.00000001985 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) plastid 0.000000000001503 Informative Direct
Cellular Component (CC) respiratory chain complex 0 Informative Direct
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.000000000000003036 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.00000000000003913 Informative Direct
Cellular Component (CC) mitochondrial intermembrane space 0.0001682 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-CH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Acting on NADH or NADPH0Moderately InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.03282Moderately InformativeInherited
Enzyme Commission (EC)NADH:ubiquinone reductase (H(+)-translocating)0InformativeDirect
Enzyme Commission (EC)With other acceptors0InformativeDirect
Enzyme Commission (EC)With other acceptors0.000000000005336InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0.000003125InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.008311InformativeInherited
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase (ubiquinone)0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.0000000001187Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0000000002174Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase0.0000000277Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processLipid metabolism0.8922Moderately InformativeInherited
Biological processIon transport1Moderately InformativeInherited
Biological processAromatic hydrocarbons catabolism0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processTricarboxylic acid cycle0InformativeDirect
Biological processSteroid metabolism0.0000000003422InformativeDirect
Biological processNitrogen fixation0.000001507InformativeDirect
Biological processAbscisic acid biosynthesis0Highly InformativeDirect
Biological processSodium transport0Highly InformativeDirect
Biological processAuxin biosynthesis0Highly InformativeDirect
Biological processCholesterol metabolism0.0000000000007489Highly InformativeDirect
Biological processPurine metabolism0.00000005098Highly InformativeDirect
Cellular componentMembrane0.0000008992Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.3715Moderately InformativeInherited
Cellular componentCell inner membrane3.314e-16InformativeDirect
Cellular componentPeroxisome0.00000000005277InformativeDirect
Cellular componentMitochondrion inner membrane0.0000001006InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular functionMolybdenum0InformativeDirect
Molecular functionSodium0InformativeDirect
Molecular functionFAD0.0000004987InformativeDirect
Molecular functionUbiquinone0Highly InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationQuinone0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001041 SSF54292 Protein matches
Abstract

The ferredoxin protein family are electron carrier proteins with an iron-sulphur cofactor that act in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s) and according to sequence similarities.

This entry represents members of the 2Fe-2S ferredoxin family that have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin and terpredoxin, and adrenodoxin [PubMed11173487, PubMed15755454, PubMed10220356, PubMed12069587]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase iron-sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).


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-quality) · Gene Ontology (high-coverage) · 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 37 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 2Fe-2S ferredoxin-like 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 37 hidden Markov models representing the 2Fe-2S ferredoxin-like 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]