6YHZ | pdb_00006yhz

UvrD helicase RNA polymerase interactions are governed by UvrDs carboxy terminal Tudor domain.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CarD-like	8040336	3000361	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CarD_CdnL_TRCF	e6yhzA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CarD_CdnL_TRCF	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02559	CarD-like/TRCF RID domain (CarD_TRCF_RID)	CarD-like/TRCF RID domain	This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvat ...	This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvation-inducible genes [1]. It interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus [4]. CarD is widely distributed among bacteria and represents a distinct class of RNAP binding proteins that regulate transcription and essential processes [4-8]. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Transcription-repair-coupling factor	hydrolase activity catalytic activity DNA binding binding damaged DNA binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding hydrolase activity catalytic activity DNA binding binding damaged DNA binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA DNA translocase activity catalytic activity, acting on a nucleic acid ATP-dependent activity RNA polymerase binding protein binding RNA polymerase core enzyme binding enzyme binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process transcription-coupled nucleotide-excision repair primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleotide-excision repair metabolic process macromolecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process transcription-coupled nucleotide-excision repair primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleotide-excision repair metabolic process macromolecule metabolic process DNA repair regulation of cellular process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process nucleotide-excision repair, DNA damage recognition chromosome organization cellular component organization organelle organization transcription-coupled nucleotide-excision repair, DNA damage recognition cellular component organization or biogenesis cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex assembly protein-containing complex organization nucleotide-excision repair, preincision complex assembly protein-DNA complex assembly	protein-containing complex catalytic complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036101	CarD-like/TRCF, RNAP-interacting domain superfamily	Homologous Superfamily
A	IPR037235	TRCF-like, C-terminal D7 domain	Homologous Superfamily
A	IPR048635	Transcription-repair-coupling factor, D3 domain	Domain
A	IPR011545	DEAD/DEAH-box helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR005118	Transcription-repair-coupling factor, C-terminal domain	Domain
A	IPR004576	Transcription-repair coupling factor	Family
A	IPR041471	UvrB, interaction domain	Domain
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR047112	ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor	Family
A	IPR003711	CarD-like/TRCF, RNAP-interacting domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.