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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 (2,474) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,297 28,899 14
Proteins 5,487 22,658 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 process0.000000073490Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.00000022730Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.00000056780Least InformativeDirect
Biological Process (BP)primary metabolic process0.000062320Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000075470Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000017930Least InformativeDirect
Biological Process (BP)biosynthetic process0.00000039370.1166Least InformativeInherited
Biological Process (BP)RNA metabolic process0.00000000000071480.000001527Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000000000049440.0004255Moderately InformativeDirect
Biological Process (BP)nucleobase-containing compound biosynthetic process0.00000000000011660.005919Moderately InformativeInherited
Biological Process (BP)gene expression0.000000000011630.001512Moderately InformativeInherited
Biological Process (BP)transcription, DNA-templated00.00003386InformativeDirect
Molecular Function (MF)transferase activity0.00000014960.6918Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.0000000000036790.0000000126Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA polymerase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.41350.05399Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.18650.00001214Least InformativeInherited
Cellular Component (CC)nuclear part0.0024390.0000000004212Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0051680.0000000000002661Moderately InformativeInherited
Cellular Component (CC)transferase complex0.0000000000000027780.2707Moderately InformativeInherited
Cellular Component (CC)DNA-directed RNA polymerase complex0.00000011210.000000000000003057InformativeDirect
Cellular Component (CC)DNA polymerase complex00.00000000001516Highly 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) response to stimulus 0.02534 Least Informative Inherited
Biological Process (BP) biological regulation 0.2831 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.004684 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.1166 Least Informative Inherited
Biological Process (BP) response to stress 0.000005414 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000001527 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0004255 Moderately Informative Direct
Biological Process (BP) organelle organization 0.09218 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.0383 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.682 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.2556 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.005974 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing compound biosynthetic process 0.005919 Moderately Informative Inherited
Biological Process (BP) gene expression 0.001512 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1545 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.4887 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.000002186 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.00003386 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00001661 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00007443 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0651 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.004416 Informative Inherited
Biological Process (BP) response to radiation 0.00946 Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.00009551 Highly Informative Direct
Biological Process (BP) DNA recombination 0.0003366 Highly Informative Direct
Biological Process (BP) aging 0.0000002789 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000009229 Highly Informative Direct
Biological Process (BP) chromosome organization 0.000000001663 Highly Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0007138 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.00004771 Least Informative Direct
Molecular Function (MF) transferase activity 0.6918 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.0000000126 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.00000000000001247 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.2408 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.00000000000007356 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) ATPase activity 0.0127 Informative Inherited
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0006507 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00001214 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.05399 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0000000004212 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000000002661 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.2707 Moderately Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase complex 0.000000000000003057 Informative Direct
Cellular Component (CC) chromosome 0.0004012 Informative Direct
Cellular Component (CC) nucleoplasm part 0.003128 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.00006957 Highly Informative Direct
Cellular Component (CC) nucleolus 0.00001245 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0.00000000001516 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 anhydrides0.0001755Moderately 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 damage0.00007128Moderately InformativeDirect
Biological processtRNA processing0.00000000000008887InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase0.000000000000027Highly InformativeDirect
Molecular functionDNA-binding0.000000005009Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0.0000000000001912Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase0.0000000000007351InformativeDirect

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 ]