SUPERFAMILY 1.75 HMM library and genome assignments server


DnaJ/Hsp40 cysteine-rich domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   DnaJ/Hsp40 cysteine-rich domain [ 57937]
Superfamily:   DnaJ/Hsp40 cysteine-rich domain [ 57938]
Families:   DnaJ/Hsp40 cysteine-rich domain [ 57939] (2)


Superfamily statistics
Genomes (3,157) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,343 25,611 2
Proteins 7,324 25,580 2


Functional annotation
General category Information
Detailed category Transcription

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) protein metabolic process 0.0002308 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0001933 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.388 Least Informative Inherited
Biological Process (BP) localization 0.006448 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.4343 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.1451 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1121 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1932 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.4218 Least Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 1.325e-06 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 2.477e-05 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.05166 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.00685 Moderately Informative Inherited
Biological Process (BP) regulation of programmed cell death 0.001602 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.02398 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.7494 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.396 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.2433 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8412 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.2189 Moderately Informative Inherited
Biological Process (BP) reproduction 0.02172 Moderately Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0.0001893 Informative Direct
Biological Process (BP) cellular membrane organization 0.0005559 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0008244 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0006708 Informative Direct
Biological Process (BP) negative regulation of cell death 3.209e-05 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0005063 Informative Direct
Biological Process (BP) protein localization to organelle 0.05152 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.1124 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.5771 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.00755 Informative Inherited
Biological Process (BP) cellular component movement 0.02411 Informative Inherited
Biological Process (BP) locomotion 0.01294 Informative Inherited
Biological Process (BP) localization of cell 0.01551 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.003719 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.004975 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.004812 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.003219 Informative Inherited
Biological Process (BP) sexual reproduction 0.003328 Informative Inherited
Biological Process (BP) single organism reproductive process 0.001386 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01139 Informative Inherited
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) spermatogenesis 1.43e-05 Highly Informative Direct
Biological Process (BP) negative regulation of phosphorylation 5.037e-06 Highly Informative Direct
Biological Process (BP) protein localization to mitochondrion 9.743e-11 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.003985 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.004104 Highly Informative Inherited
Molecular Function (MF) binding 0.1268 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.0004415 Moderately Informative Direct
Molecular Function (MF) unfolded protein binding 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 3.718e-06 Least Informative Direct
Cellular Component (CC) membrane 0.05643 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9054 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.164 Least Informative Inherited
Cellular Component (CC) plastid 1.018e-07 Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)lung0InformativeDirect
Xenopus ANatomical entity (XAN)skeletal system0InformativeDirect
Xenopus ANatomical entity (XAN)bone tissue0Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA replication0InformativeDirect
Biological processStress response0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationMethylation8.408e-08Moderately InformativeDirect
Post-translational modificationPrenylation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001305 SSF57938 Protein matches
Abstract

Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolyzing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold [PubMed8016869]. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.

Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation [PubMed15063739]. Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate.


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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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 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 DnaJ/Hsp40 cysteine-rich domain 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 DnaJ/Hsp40 cysteine-rich domain 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]