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HRDC-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   HRDC-like [ 47819] (4)
Families:   HRDC domain from helicases [ 47820] (2)
  RNA polymerase II subunit RBP4 (RpoF) [ 69044]
  RNase D C-terminal domains [ 140643]
  EXOSC10 HRDC domain-like [ 140646] (2)


Superfamily statistics
Genomes (2,479) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 6,315 32,657 14
Proteins 5,505 27,365 13


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process0.000000082240Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.00000025150Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.00000065990Least InformativeDirect
Biological Process (BP)primary metabolic process0.000074050Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000084440Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.0000002120Least InformativeDirect
Biological Process (BP)biosynthetic process0.00000038450.08851Least InformativeInherited
Biological Process (BP)RNA metabolic process0.00000000000079810.000001012Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000000000047590.0002454Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.000000000013510.008074Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.0000000001290.03988Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.000000000050510.01542Moderately InformativeInherited
Biological Process (BP)gene expression0.000000000013510.001116Moderately InformativeInherited
Biological Process (BP)transcription, DNA-templated00.0001008InformativeDirect
Molecular Function (MF)transferase activity0.00000015480.6752Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.0000000000040540.00000002443Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA polymerase activity00Highly InformativeDirect
Cellular Component (CC)macromolecular complex0.0000001880.000000000004005Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.19090.000007041Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.43150.04439Least InformativeInherited
Cellular Component (CC)nuclear part0.0027440.00000000004636Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0065450.00000000000006369Moderately InformativeInherited
Cellular Component (CC)transferase complex0.0000000000000026430.2101Moderately InformativeInherited
Cellular Component (CC)transferase complex, transferring phosphorus-containing groups00InformativeDirect
Cellular Component (CC)DNA polymerase complex00.00000000002668Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.08851 Least Informative Inherited
Biological Process (BP) response to stimulus 0.05506 Least Informative Inherited
Biological Process (BP) biological regulation 0.0343 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.001466 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00004806 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000001012 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0000000005537 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0002454 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.00615 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.3368 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2493 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3161 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.008074 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.05871 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.9708 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4542 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.5544 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.03988 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.01542 Moderately Informative Inherited
Biological Process (BP) gene expression 0.001116 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0000001915 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0001008 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00003667 Informative Direct
Biological Process (BP) chromosome organization 0.00000001933 Informative Direct
Biological Process (BP) regulation of cell cycle 0.0095 Informative Inherited
Biological Process (BP) response to radiation 0.01016 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.01977 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.02217 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.04282 Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.0001128 Highly Informative Direct
Biological Process (BP) aging 0.0000004923 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.0000003542 Highly Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0006037 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.001154 Highly Informative Inherited
Biological Process (BP) RNA catabolic process 0.00162 Highly Informative Inherited
Biological Process (BP) double-strand break repair 0.005173 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00005392 Least Informative Direct
Molecular Function (MF) transferase activity 0.6752 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000002443 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.00000000000004203 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.2311 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.0000000000001789 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) ATPase activity 0.01457 Informative Inherited
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0.000000000004005 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0005263 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000007041 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.04439 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000000004636 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000000000006369 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.2101 Moderately Informative Inherited
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.004814 Informative Inherited
Cellular Component (CC) chromosome 0.01066 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.00005681 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0.00000000002668 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on acid anhydrides0.0005332Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.001517Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)syndrome0Moderately InformativeDirect

Document: DO 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)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately 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)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.0001694Moderately InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0.00001584Moderately InformativeDirect
Biological processtRNA processing0.0000000000001264InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase0.00000000000002539Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0.0000000000001791Moderately InformativeDirect
Post-translational modificationDNA-binding0.000000004681Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase0.0000000000006722InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010997 SSF47819 Protein matches
Abstract

The HRDC (helicase and RNaseD C-terminal) domain is comprised of two orthogonally packed alpha-hairpin subdomains, and is involved in interactions with DNA and protein.

The HRDC (helicase and RNaseD C-terminal) domain is found at the C terminus of many RecQ helicases, including the human Werner and Bloom syndrome proteins [PubMed10647186]. RecQ helicases have been shown to unwind DNA in an ATP-dependent manner. The structure of the HRDC domain consists of a 4-5 helical bundle of two orthogonally packed alpha-hairpins, and as such it resembles auxiliary domains in bacterial DNA helicases and other proteins that interact with nucleic acids. A positively charged region on the surface of the HRDC domain is able to interact with DNA.

The HRDC domain is also present in eukaryotic and archaeal RNA polymerase II subunit RBP4, the N-terminal of which forms a heterodimerisation alpha-hairpin [PubMed15591044, PubMed11741548].


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 10 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 HRDC-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 10 hidden Markov models representing the HRDC-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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]