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  Home > SCOP hierarchy > YggX-like superfamily


YggX-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   YggX-like [ 111147]
Superfamily:   YggX-like [ 111148]
Families:   YggX-like [ 111149] (2)

Superfamily statistics
Genomes (750) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 752 5,423 2
Proteins 752 5,421 2

 Functional annotation
General category General
Detailed category General

Document: Function annotation of SCOP domain superfamilies

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Molecular functionIron0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR007457 SSF111148 Protein matches
Abstract

The protein represented by this entry, YggX, serves to protect Fe-S clusters from oxidative damage [PubMed11416172]. The effect is two-fold: proteins that rely on Fe-S clusters do not become inactivated, and the release of free iron and hydrogen peroxide--a DNA damaging agent--is prevented. These observations are consistent with the hypothesis that YggX chelates free iron, and recent experiments show that YggX can indeed bind Fe(II) in vitro and in vivo [PubMed12670952]. Furthermore, YggX has a positive effect on the action of at least one Fe(II)-responsive protein. The combined actions of YggX is reminiscent of iron trafficking proteins [PubMed12033438], and YggX is therefore proposed to play a role in Fe(II) trafficking [PubMed12670952]. In Escherichia coli, YggX was shown to be under the transcriptional control of the redox-sensing SoxRS system [PubMed14594836].


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 · 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 YggX-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 4 hidden Markov models representing the YggX-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 · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.