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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 (2,481) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 6,328 32,657 14
Proteins 5,518 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 process0.000000068670Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.00000021260Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.00000061160Least InformativeDirect
Biological Process (BP)primary metabolic process0.000064840Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000070670Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000000180Least InformativeDirect
Biological Process (BP)biosynthetic process0.00000032420.108Least InformativeInherited
Biological Process (BP)gene expression0.000000000013930.000675Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.00000000000067390.000000423Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000000000040130.0003657Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000000000110.04644Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.000000000041850.01806Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.000000000011270.009604Moderately InformativeInherited
Biological Process (BP)transcription, DNA-templated00.0001298InformativeDirect
Molecular Function (MF)transferase activity0.00000013730.6827Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.0000000000038260.00000003517Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA polymerase activity00Highly InformativeDirect
Cellular Component (CC)intracellular organelle part0.18680.00001511Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.42810.04441Least InformativeInherited
Cellular Component (CC)transferase complex0.0000000000000026290.218Moderately InformativeInherited
Cellular Component (CC)nuclear part0.0029120.00000000005229Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.006620.0000000000001875Moderately InformativeInherited
Cellular Component (CC)transferase complex, transferring phosphorus-containing groups00InformativeDirect
Cellular Component (CC)DNA polymerase complex00.00000000002574Highly 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) cellular component organization or biogenesis 0.0001629 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.05755 Least Informative Inherited
Biological Process (BP) biological regulation 0.02297 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.108 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.0002726 Moderately Informative Direct
Biological Process (BP) gene expression 0.000675 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000423 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000000003306 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0003657 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.9883 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.01047 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.05407 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.4305 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.3262 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.4128 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.04644 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.01806 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.009604 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.1498 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.4661 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.00000004968 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0001298 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00002464 Informative Direct
Biological Process (BP) growth 0.0002294 Informative Direct
Biological Process (BP) chromosome organization 0.0000000002828 Informative Direct
Biological Process (BP) regulation of cell cycle 0.01544 Informative Inherited
Biological Process (BP) response to radiation 0.01058 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.01828 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.009109 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.02045 Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.0001138 Highly Informative Direct
Biological Process (BP) aging 0.000000631 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000004278 Highly Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0005395 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.001532 Highly Informative Inherited
Biological Process (BP) RNA catabolic process 0.001982 Highly Informative Inherited
Biological Process (BP) double-strand break repair 0.005412 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00005393 Least Informative Direct
Molecular Function (MF) binding 0.09722 Least Informative Inherited
Molecular Function (MF) transferase activity 0.6827 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000003517 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.00000000000006382 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.00003136 Moderately Informative Direct
Molecular Function (MF) anion binding 0.7322 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.009238 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.03422 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.2335 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.002835 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.0000000000001809 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.0006473 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.0007334 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0003069 Informative Direct
Molecular Function (MF) ATPase activity 0.0149 Informative Inherited
Molecular Function (MF) DNA binding 0.07897 Informative Inherited
Molecular Function (MF) single-stranded DNA binding 0.00001174 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0000449 Highly Informative Direct
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0005548 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00001511 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.04441 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000000005229 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000000001875 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.218 Moderately Informative Inherited
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.004313 Informative Inherited
Cellular Component (CC) chromosome 0.009341 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.00005065 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0.00000000002574 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0.00001557Moderately InformativeDirect
Biological processtRNA processing0.0000000000001203InformativeDirect
Biological processDNA repair0.0000006011InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase0.00000000000002417Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0.0000000000001761Moderately InformativeDirect
Post-translational modificationDNA-binding0.000000004839Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase0.0000000000006611InformativeDirect
Post-translational modificationIsopeptide bond0.00007317Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0006204Moderately InformativeDirect

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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]