SUPERFAMILY 1.75 HMM library and genome assignments server


Head domain of nucleotide exchange factor GrpE superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Head domain of nucleotide exchange factor GrpE [ 51063]
Superfamily:   Head domain of nucleotide exchange factor GrpE [ 51064]
Families:   Head domain of nucleotide exchange factor GrpE [ 51065]


Superfamily statistics
Genomes (3,106) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,585 0 1
Proteins 3,583 0 1


Functional annotation
General category General
Detailed category General

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 cellular process 0.2859 Least Informative Inherited
Biological Process (BP) localization 0.02669 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01284 Least Informative Inherited
Biological Process (BP) organelle organization 0.0002493 Moderately Informative Direct
Biological Process (BP) macromolecule localization 3.572e-05 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0001924 Moderately Informative Direct
Biological Process (BP) organic substance transport 3.017e-05 Moderately Informative Direct
Biological Process (BP) mitochondrion organization 1.543e-06 Informative Direct
Biological Process (BP) protein transport 3.382e-07 Informative Direct
Biological Process (BP) cytoplasmic transport 1.084e-07 Informative Direct
Biological Process (BP) protein localization to organelle 1.686e-08 Informative Direct
Biological Process (BP) mitochondrial transport 3.014e-12 Highly Informative Direct
Biological Process (BP) protein localization to mitochondrion 2.766e-14 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 8.94e-11 Highly Informative Direct
Molecular Function (MF) binding 0.005298 Least Informative Inherited
Molecular Function (MF) unfolded protein binding 5.315e-14 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0002222 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000431 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.1471 Least Informative Inherited
Cellular Component (CC) mitochondrial part 2.675e-05 Moderately Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processStress response0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Post-translational modificationChaperone0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009012 SSF51064 Protein matches
Abstract

In prokaryotes, the nucleotide exchange factor GrpE and the chaperone DnaJ are required for nucleotide binding of the molecular chaperone DnaK [PubMed9103205]. The DnaK reaction cycle involves rapid peptide binding and release, which is dependent upon nucleotide binding. DnaJ accelerates the hydrolysis of ATP by DnaK, which enables the ADP-bound DnaK to tightly bind peptide. GrpE catalyses the release of ADP from DnaK, which is required for peptide release. In eukaryotes, GrpE is essential for mitochondrial Hsp70 function, however the cytosolic Hsp70 homologues are GrpE-independent.

GrpE binds as a homodimer to the ATPase domain of DnaK, and may interact with the peptide-binding domain of DnaK. GrpE accomplishes nucleotide exchange by opening the nucleotide-binding cleft of DnaK. GrpE is comprised of two domains, the N-terminal coiled coil domain, which may facilitate peptide release, and the C-terminal head domain, which forms part of the contact surface with the ATPase domain of DnaK. The head domain is comprised of six short beta strands with a limited hydrophobic core.


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) · Arabidopsis Plant Ontology (AP) · 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 1 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 Head domain of nucleotide exchange factor GrpE 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 1 hidden Markov models representing the Head domain of nucleotide exchange factor GrpE 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]