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 (1,958)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	5,125	13,308	14
Proteins	4,484	10,542	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 term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	cellular aromatic compound metabolic process	1.994e-09	0	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	2.08e-08	0	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	1.157e-08	0	Least Informative	Direct
Biological Process (BP)	heterocycle metabolic process	1.751e-09	0	Least Informative	Direct
Biological Process (BP)	organic cyclic compound metabolic process	4.889e-09	0	Least Informative	Direct
Biological Process (BP)	biosynthetic process	6.131e-09	0.01023	Least Informative	Inherited
Biological Process (BP)	RNA metabolic process	2.614e-14	0.0001011	Moderately Informative	Direct
Biological Process (BP)	cellular macromolecule biosynthetic process	1.399e-13	6.471e-06	Moderately Informative	Direct
Biological Process (BP)	heterocycle biosynthetic process	2.521e-13	0.00796	Moderately Informative	Inherited
Biological Process (BP)	aromatic compound biosynthetic process	7.849e-14	0.007273	Moderately Informative	Inherited
Biological Process (BP)	cellular nitrogen compound biosynthetic process	3.515e-13	0.01003	Moderately Informative	Inherited
Biological Process (BP)	organic cyclic compound biosynthetic process	8.047e-13	0.02537	Moderately Informative	Inherited
Biological Process (BP)	gene expression	2.621e-13	0.001125	Moderately Informative	Inherited
Biological Process (BP)	transcription, DNA-dependent	0	8.666e-05	Informative	Direct
Molecular Function (MF)	transferase activity	2.515e-10	0.2954	Least Informative	Inherited
Molecular Function (MF)	transferase activity, transferring phosphorus-containing groups	4.126e-14	9.498e-08	Moderately Informative	Direct
Molecular Function (MF)	nucleotidyltransferase activity	0	0	Informative	Direct
Molecular Function (MF)	RNA polymerase activity	0	0	Highly Informative	Direct
Cellular Component (CC)	protein complex	1.436e-10	7.003e-11	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	0.379	2.668e-07	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.04826	0.1165	Least Informative	Inherited
Cellular Component (CC)	nuclear part	0.0004733	1.186e-12	Moderately Informative	Direct
Cellular Component (CC)	intracellular organelle lumen	0.0004157	6.015e-10	Moderately Informative	Direct
Cellular Component (CC)	DNA-directed RNA polymerase complex	3.805e-08	1.146e-13	Informative	Direct
Cellular Component (CC)	DNA polymerase complex	0	4.216e-12	Highly Informative	Direct

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)	nitrogen compound metabolic process	0	Least Informative	Direct
Biological Process (BP)	cellular macromolecule 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)	regulation of cellular process	1	Least Informative	Inherited
Biological Process (BP)	developmental process	0.4223	Least Informative	Inherited
Biological Process (BP)	multicellular organismal process	0.8981	Least Informative	Inherited
Biological Process (BP)	regulation of metabolic process	0.009706	Least Informative	Inherited
Biological Process (BP)	biosynthetic process	0.01023	Least Informative	Inherited
Biological Process (BP)	response to stimulus	0.008869	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	0.7001	Least Informative	Inherited
Biological Process (BP)	cellular component organization or biogenesis	0.01127	Least Informative	Inherited
Biological Process (BP)	RNA metabolic process	0.0001011	Moderately Informative	Direct
Biological Process (BP)	cellular response to stress	3.038e-09	Moderately Informative	Direct
Biological Process (BP)	cellular macromolecule biosynthetic process	6.471e-06	Moderately Informative	Direct
Biological Process (BP)	homeostatic process	0.0009136	Moderately Informative	Direct
Biological Process (BP)	negative regulation of cellular process	0.1022	Moderately Informative	Inherited
Biological Process (BP)	regulation of nitrogen compound metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	negative regulation of metabolic process	0.3749	Moderately Informative	Inherited
Biological Process (BP)	regulation of gene expression	1	Moderately Informative	Inherited
Biological Process (BP)	single-organism developmental process	0.6047	Moderately Informative	Inherited
Biological Process (BP)	response to abiotic stimulus	0.02565	Moderately Informative	Inherited
Biological Process (BP)	heterocycle biosynthetic process	0.00796	Moderately Informative	Inherited
Biological Process (BP)	aromatic compound biosynthetic process	0.007273	Moderately Informative	Inherited
Biological Process (BP)	cellular nitrogen compound biosynthetic process	0.01003	Moderately Informative	Inherited
Biological Process (BP)	organic cyclic compound biosynthetic process	0.02537	Moderately Informative	Inherited
Biological Process (BP)	gene expression	0.001125	Moderately Informative	Inherited
Biological Process (BP)	cellular catabolic process	0.02236	Moderately Informative	Inherited
Biological Process (BP)	organic substance catabolic process	0.05239	Moderately Informative	Inherited
Biological Process (BP)	organelle organization	0.04395	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular metabolic process	0.8664	Moderately Informative	Inherited
Biological Process (BP)	DNA metabolic process	1.102e-06	Informative	Direct
Biological Process (BP)	transcription, DNA-dependent	8.666e-05	Informative	Direct
Biological Process (BP)	response to DNA damage stimulus	2.196e-05	Informative	Direct
Biological Process (BP)	regulation of cell cycle process	0.0001282	Informative	Direct
Biological Process (BP)	cellular macromolecule catabolic process	0.0007626	Informative	Direct
Biological Process (BP)	chromosome organization	1.795e-07	Informative	Direct
Biological Process (BP)	anatomical structure homeostasis	4.057e-09	Informative	Direct
Biological Process (BP)	negative regulation of cellular metabolic process	0.03176	Informative	Inherited
Biological Process (BP)	negative regulation of nitrogen compound metabolic process	0.008036	Informative	Inherited
Biological Process (BP)	nucleobase-containing compound catabolic process	0.01337	Informative	Inherited
Biological Process (BP)	DNA catabolic process	0.0001295	Highly Informative	Direct
Biological Process (BP)	aging	4.017e-07	Highly Informative	Direct
Biological Process (BP)	response to ionizing radiation	0.0001635	Highly Informative	Direct
Biological Process (BP)	regulation of gene expression, epigenetic	3.257e-06	Highly Informative	Direct
Biological Process (BP)	regulation of DNA metabolic process	5.805e-06	Highly Informative	Direct
Biological Process (BP)	nucleic acid phosphodiester bond hydrolysis	0.008979	Highly Informative	Inherited
Biological Process (BP)	DNA repair	0.004871	Highly Informative	Inherited
Molecular Function (MF)	hydrolase activity	0.0008204	Least Informative	Direct
Molecular Function (MF)	transferase activity	0.2954	Least Informative	Inherited
Molecular Function (MF)	transferase activity, transferring phosphorus-containing groups	9.498e-08	Moderately Informative	Direct
Molecular Function (MF)	hydrolase activity, acting on ester bonds	0.501	Moderately Informative	Inherited
Molecular Function (MF)	nuclease activity	7.029e-10	Informative	Direct
Molecular Function (MF)	nucleotidyltransferase activity	0	Informative	Direct
Molecular Function (MF)	nucleoside-triphosphatase activity	1.03e-13	Informative	Direct
Molecular Function (MF)	RNA polymerase activity	0	Highly Informative	Direct
Cellular Component (CC)	intracellular non-membrane-bounded organelle	1.905e-07	Least Informative	Direct
Cellular Component (CC)	protein complex	7.003e-11	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	2.668e-07	Least Informative	Direct
Cellular Component (CC)	intracellular membrane-bounded organelle	0.1165	Least Informative	Inherited
Cellular Component (CC)	nuclear part	1.186e-12	Moderately Informative	Direct
Cellular Component (CC)	intracellular organelle lumen	6.015e-10	Moderately Informative	Direct
Cellular Component (CC)	DNA-directed RNA polymerase complex	1.146e-13	Informative	Direct
Cellular Component (CC)	nucleoplasm part	0.2676	Informative	Inherited
Cellular Component (CC)	chromosome	0.04992	Informative	Inherited
Cellular Component (CC)	DNA-directed RNA polymerase II, core complex	2.539e-06	Highly Informative	Direct
Cellular Component (CC)	DNA polymerase complex	4.216e-12	Highly Informative	Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Acting on acid anhydrides	0.0005332	Least Informative	Direct
Enzyme Commission (EC)	Acting on ester bonds	0.001517	Least Informative	Inherited
Enzyme Commission (EC)	Acting on acid anhydrides; involved in cellular an	0	Moderately Informative	Direct

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)

	DO term	FDR (all)	SDDO level	Annotation (direct or inherited)
Disease Ontology (DO)	syndrome	0	Moderately Informative	Direct

Document: DO annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)

	YP term	FDR (all)	SDYP level	Annotation (direct or inherited)
Yeast Phenotype (YP)	resistance to chemicals	0	Least Informative	Direct

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)

	FP term	FDR (all)	SDFP level	Annotation (direct or inherited)
Fly Phenotype (FP)	lethal	0	Least Informative	Direct

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)

	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	cell	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	viscus	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	portion of tissue	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	gamete	0	Moderately Informative	Direct

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	shoot apex	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	C globular stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	Least Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Hydrolases	0	Least Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides	0.0005169	Moderately Informative	Direct
Enzyme Commission (EC)	Exoribonucleases producing 5'-phosphomonoesters	0	Informative	Direct
Enzyme Commission (EC)	DNA helicase	0	Informative	Direct

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	DNA damage	6.417e-05	Moderately Informative	Direct
Biological process	tRNA processing	2.742e-14	Informative	Direct
Biological process	DNA-directed RNA polymerase	1.963e-11	Highly Informative	Direct
Cellular component	Nucleus	0	Least Informative	Direct
Molecular function	Nucleotide-binding	0.005286	Least Informative	Inherited
Molecular function	DNA-binding	5.143e-10	Moderately Informative	Direct
Molecular function	Helicase	0	Informative	Direct
Post-translational modification	Hydrolase	0	Least Informative	Direct
Post-translational modification	Nuclease	1.172e-12	Moderately Informative	Direct
Post-translational modification	Exonuclease	0	Informative	Direct

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 [ PubMed 10647186]. 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 [ PubMed 15591044, PubMed 11741548].

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.

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HRDC-like superfamily