3HJH

A rigid N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3hjha1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8037544	3002019	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	PF17757	e3hjhA2	A: beta meanders	X: Colicin E3 ribonuclease domain-like	H: UvrB interaction domain (From Topology)	T: UvrB interaction domain	F: PF17757	ECOD (1.6)
A	F_UNCLASSIFIED	e3hjhA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF21132	e3hjhA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF21132	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.11180	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.2060.10	Alpha Beta	2-Layer Sandwich	Penicillin-binding protein 1b fold	Penicillin-binding protein 1b domain	CATH (4.3.0)
A	3.40.50.11140	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21132	MFD, D3 domain (MFD_D3)	MFD, D3 domain	The transcription-repair coupling factor (TRCF, also known as MFD) couples transcription and DNA repair in bacteria. MFD removes transcription elongation complexes stalled at DNA lesions and recruits the nucleotide excision repair (NER) machinery to ...	The transcription-repair coupling factor (TRCF, also known as MFD) couples transcription and DNA repair in bacteria. MFD removes transcription elongation complexes stalled at DNA lesions and recruits the nucleotide excision repair (NER) machinery to the site [3]. This protein consists of eight domains [3,4], of which D3 is represented in this entry and its function is unknown. This domain plays a critical role in unmasking of the UvrA binding site [3].	Domain
A	PF17757	UvrB interaction domain (UvrB_inter)	UvrB interaction domain	This domain is found in the UvrB protein where it interacts with the UvrA protein [2].	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 organic cyclic compound 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 hydrolase activity catalytic activity DNA binding binding organic cyclic compound 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 organic cyclic compound metabolic process organic substance metabolic process nucleotide-excision repair 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 organic cyclic compound metabolic process organic substance metabolic process nucleotide-excision repair metabolic process macromolecule metabolic process DNA repair regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process cellular component organization transcription-coupled nucleotide-excision repair, DNA damage recognition cellular component organization or biogenesis nucleotide-excision repair, DNA damage recognition chromosome organization organelle organization 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 intracellular anatomical structure cytoplasm cellular anatomical entity 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 National Science Foundation (DBI-1832184), 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 R01GM133198.