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alpha-helical ferredoxin superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Globin-like [ 46457] (2)
Superfamily:   alpha-helical ferredoxin [ 46548] (2)
Families:   Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain [ 46549] (2)
  Dihydropyrimidine dehydrogenase, N-terminal domain [ 46553]


Superfamily statistics
Genomes (2,997) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 14,885 89,370 6
Proteins 14,538 86,766 6


Functional annotation
General category Metabolism
Detailed category Redox

Document:
Function annotation of SCOP domain superfamilies

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) single-organism cellular process 0.000000003288 Least Informative Direct
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.5013 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.559 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.914 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.648 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.2319 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5236 Least Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.0000000000001125 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.00005825 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.00009974 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.8486 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.475 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2087 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.2218 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.1987 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.001173 Moderately Informative Inherited
Biological Process (BP) cellular respiration 0 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.00000000000001422 Informative Direct
Biological Process (BP) electron transport chain 0.0000000001353 Informative Direct
Biological Process (BP) ATP metabolic process 0.00000002613 Informative Direct
Biological Process (BP) dicarboxylic acid metabolic process 0.0000006643 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.00002344 Informative Direct
Biological Process (BP) glycosyl compound metabolic process 0.00006995 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.000198 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0002531 Informative Direct
Biological Process (BP) phosphorylation 0.003549 Informative Inherited
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) citrate metabolic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) dicarboxylic acid biosynthetic process 0.00000000006013 Highly Informative Direct
Biological Process (BP) nucleoside catabolic process 0.00000000006856 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.00003012 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.4018 Highly Informative Inherited
Molecular Function (MF) binding 0.9605 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) electron carrier activity 0.000000000000005506 Informative Direct
Molecular Function (MF) iron-sulfur cluster binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0.00003506 Highly Informative Direct
Cellular Component (CC) protein complex 0.00000005471 Least Informative Direct
Cellular Component (CC) membrane 0.000228 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.08087 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.3664 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.8752 Least Informative Inherited
Cellular Component (CC) mitochondrial protein complex 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) organelle inner membrane 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial envelope 0.000000000000003036 Moderately 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 0.00000001406 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0000001052 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 a sulfur group of donors0.01252Moderately InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH0.3724Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.08933Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)With other acceptors0.000000003239InformativeDirect
Enzyme Commission (EC)With other acceptors0.0000004674InformativeDirect
Enzyme Commission (EC)Dihydropyrimidine dehydrogenase (NADP(+))0Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors0Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase (ubiquinone)0Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase (quinone)0.0000001776Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADH)0.0000001803Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADPH)0.00000537Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processTricarboxylic acid cycle0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processMethanogenesis0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0.00000000003664Moderately InformativeDirect
Cellular componentCell membrane0.00002667Moderately InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransit peptide0.000005892Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionFlavoprotein0.001698Moderately InformativeInherited
Molecular function2Fe-2S0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionNickel0.0000000000003884InformativeDirect
Molecular functionFAD0.0000000007629InformativeDirect
Molecular functionFMN0.0002523InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationQuinone0.000005936Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009051 SSF46548 Protein matches
Abstract

The alpha-helical ferredoxin domain contains two Fe4-S4 clusters, typical of bacterial ferredoxin. Iron-sulphur proteins play an important role in electron transfer processes and in various enzymatic reactions. In eukaryotes, the mitochondria are the major site of Fe-S cluster biosynthesis in the cell, used for the assembly of mitochondrial and non-mitochondrial Fe-S proteins. The alpha-helical ferredoxin domain is present in several proteins involved in redox reactions, including the C-terminal of the respiratory proteins succinate dehydrogenase (SQR) in bacteria/mitochondria, and fumarate reductase (QFR) in bacteria. SQR is analogous to the mitochondrial respiratory complex II, and is involved in the electron transport pathway from succinate as a donor to the acceptor ubiquinone. SQR helps prevent the formation of reactive oxygen species and is used during aerobic respiration, whereas QFR does not and, consequently, is used to catalyse the final step of anaerobic respiration using the acceptor fumarate [PubMed11850430].

The alpha-helical ferredoxin domain is also present in the N-terminal of the cytosolic protein dihydropyrimidine dehydrogenase, (DPD) which catalyses the NADPH-dependent, rate-limiting step in pyrimidine degradation, converting pyrimidines to 5,6-dihydro compounds [PubMed11796730]. DPD catalysis involves electron transfer from NADPH to the substrate via the Fe4-S4 centre and FAD. In mammals, this pathway produces the neurotransmitter beta-alanine.


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) · 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 4 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 alpha-helical ferredoxin 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 4 hidden Markov models representing the alpha-helical ferredoxin 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) · UniProtKB KeyWords (KW) · Internal database links ]