SUPERFAMILY 1.75 HMM library and genome assignments server


GntR ligand-binding domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   GntR ligand-binding domain-like [ 48007]
Superfamily:   GntR ligand-binding domain-like [ 48008]
Families:   GntR ligand-binding domain-like [ 48009] (2)


Superfamily statistics
Genomes (1,689) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,893 37,851 3
Proteins 12,839 37,763 3


Functional annotation
General category Regulation
Detailed category DNA-binding

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) regulation of metabolic process 3.356e-08 Least Informative Direct
Biological Process (BP) regulation of cellular process 9.282e-06 Least Informative Direct
Biological Process (BP) regulation of gene expression 4.507e-09 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1.391e-09 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1.922e-10 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.03275 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 9.036e-07 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 8.834e-07 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processLipid metabolism0Moderately InformativeDirect
Biological processFatty acid metabolism0InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008920 SSF48008 Protein matches
Abstract

Bacteria regulate membrane fluidity by manipulating the relative levels of saturated and unsaturated fatty acids within the phospholipids of their membrane bilayers. In Escherichia coli, the transcription factor, FadR, functions as a switch that co-ordinately regulates the machinery required for fatty acid beta-oxidation and the expression of a key enzyme in fatty acid biosynthesis. This single repressor controls the transcription of the whole fad regulon [PubMed11279025]. Binding of fadR is specifically inhibited by long chain fatty acyl-CoA compounds.

The crystal structure of FadR reveals a two domain dimeric molecule where the N-terminal winged-helix domain binds DNA , and the C-terminal domain binds acyl-CoA [PubMed11279025]. The binding of acyl-CoA to the C-terminal domain results in a conformational change that affects the DNA binding affinity of the N-terminal domain [PubMed11013219].

FadR is a member of the GntR family of bacterial transcription regulators. The DNA-binding domain is well conserved for this family, whereas the C-terminal effector-binding domain is more variable, and is consequently used to define the GntR subfamilies [PubMed11756427]. The FadR group is the largest subgroup, and is characterised by an all-helical C-terminal domain composed of 6 to 7 alpha helices [PubMed11013219]. This entry represents the C-terminal domain of FadR.


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) · 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 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 GntR ligand-binding domain-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 2 hidden Markov models representing the GntR ligand-binding domain-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-coverage) · UniProtKB KeyWords (KW) · Internal database links ]