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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 (2,999) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 14,907 117,983 6
Proteins 14,560 114,733 6


Functional annotation
General category Metabolism
Detailed category Redox

Document:
Function annotation of SCOP domain superfamilies

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

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage0.00000007007InformativeDirect

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 CH or CH(2) groups0.0000003863InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0.00894InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.00938InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.5649InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH0.748InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With a quinone or related compound as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase (quinone)0.0000006107Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0.0001964Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1Highly InformativeInherited

Document: EC 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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Arabidopsis Plant Ontology (AP) · 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 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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]