2EYQ

Crystal structure of Escherichia coli 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	d2eyqa1	All beta proteins	SH3-like barrel	CarD-like	CarD-like	Transcription-repair coupling factor, RRCF, middle domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2eyqa4	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Transcription-repair coupling factor TRCF, domain 1	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2eyqa2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Transcription-repair coupling factor TRCF, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2eyqa3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Transcription-repair coupling factor TRCF, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2eyqa5	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Transcription-repair coupling factor TRCF, domain 4	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2eyqa6	Alpha and beta proteins (a+b)	TRCF domain-like	TRCF domain-like	TRCF domain	Transcription-repair coupling factor, TRCF, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2eyqb1	All beta proteins	SH3-like barrel	CarD-like	CarD-like	Transcription-repair coupling factor, RRCF, middle domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2eyqb4	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Transcription-repair coupling factor TRCF, domain 1	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2eyqb2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Transcription-repair coupling factor TRCF, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2eyqb3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Transcription-repair coupling factor TRCF, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2eyqb5	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Transcription-repair coupling factor TRCF, domain 4	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2eyqb6	Alpha and beta proteins (a+b)	TRCF domain-like	TRCF domain-like	TRCF domain	Transcription-repair coupling factor, TRCF, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	TRCF domain	8027960	4003810	SCOP2 (2022-06-29)
A	SCOP2 Family	CarD-like	8027957	4001778	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TRCF domain-like	8040339	3001539	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CarD-like	8040336	3000361	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8037544	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CarD-like	8040336	3000361	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TRCF domain-like	8040339	3001539	SCOP2B (2022-06-29)
B	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	CarD_CdnL_TRCF	e2eyqA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CarD_CdnL_TRCF	ECOD (1.6)
A	UB2H_1	e2eyqA3	A: beta meanders	X: Colicin E3 ribonuclease domain-like	H: UvrB interaction domain (From Topology)	T: UvrB interaction domain	F: UB2H_1	ECOD (1.6)
A	TRCF	e2eyqA2	A: a+b two layers	X: TRCF domain (From Topology)	H: TRCF domain (From Topology)	T: TRCF domain	F: TRCF	ECOD (1.6)
A	DEAD	e2eyqA5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
A	PRK10689	e2eyqA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PRK10689	ECOD (1.6)
A	ResIII	e2eyqA7	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ResIII	ECOD (1.6)
A	Helicase_C_9	e2eyqA6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_9	ECOD (1.6)
B	CarD_CdnL_TRCF	e2eyqB8	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CarD_CdnL_TRCF	ECOD (1.6)
B	UB2H_1	e2eyqB3	A: beta meanders	X: Colicin E3 ribonuclease domain-like	H: UvrB interaction domain (From Topology)	T: UvrB interaction domain	F: UB2H_1	ECOD (1.6)
B	TRCF	e2eyqB2	A: a+b two layers	X: TRCF domain (From Topology)	H: TRCF domain (From Topology)	T: TRCF domain	F: TRCF	ECOD (1.6)
B	DEAD	e2eyqB5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
B	PRK10689	e2eyqB7	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PRK10689	ECOD (1.6)
B	ResIII	e2eyqB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ResIII	ECOD (1.6)
B	Helicase_C_9	e2eyqB6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_9	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)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.10.170	Mainly Beta	Beta Barrel	Thrombin, subunit H		CATH (4.3.0)
A	3.90.1150.50	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Transcription-repair-coupling factor, D7 domain	CATH (4.3.0)
B	3.40.50.11180	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.2060.10	Alpha Beta	2-Layer Sandwich	Penicillin-binding protein 1b fold	Penicillin-binding protein 1b domain	CATH (4.3.0)
B	3.40.50.11140	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.40.10.170	Mainly Beta	Beta Barrel	Thrombin, subunit H		CATH (4.3.0)
B	3.90.1150.50	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Transcription-repair-coupling factor, D7 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
A, B	PF03461	TRCF domain (TRCF)	TRCF domain	-	Domain
A, B	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A, B	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A, B	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, B	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, B	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, B	IPR036101	CarD-like/TRCF, RNAP-interacting domain superfamily	Homologous Superfamily
A, B	IPR037235	TRCF-like, C-terminal D7 domain	Homologous Superfamily
A, B	IPR048635	Transcription-repair-coupling factor, D3 domain	Domain
A, B	IPR011545	DEAD/DEAH box helicase domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR005118	Transcription-repair-coupling factor, C-terminal domain	Domain
A, B	IPR004576	Transcription-repair coupling factor	Family
A, B	IPR041471	UvrB, interaction domain	Domain
A, B	IPR001650	Helicase, C-terminal domain-like	Domain
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR047112	ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor	Family
A, B	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.