9F0Y | pdb_00009f0y

CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, derived from the ss-27_+8ds+9_+143-R Locally-refined 3.45 A Map.

External Resource: Annotation

Domain Annotation: SCOP2 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)
C	SCOP2B Superfamily	IHF-like DNA-binding proteins	8034409	3000426	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	IHF-like DNA-binding proteins	8034410	3000426	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Origin of replication-binding domain, RBD-like	8038183	3001937	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00216	Bacterial DNA-binding protein (Bac_DNA_binding)	Bacterial DNA-binding protein		Domain
D	PF00216	Bacterial DNA-binding protein (Bac_DNA_binding)	Bacterial DNA-binding protein		Domain
E [auth F], F [auth E], G	PF05509	TraY domain (TraY)	TraY domain	This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid [1]. These proteins have a ribbon-helix-helix fold and are likely to be DNA-bi ...	This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid [1]. These proteins have a ribbon-helix-helix fold and are likely to be DNA-binding proteins.	Domain
H	PF18340	DNA relaxase TraI 2B/2B-like domain (TraI_2B)	DNA relaxase TraI 2B/2B-like domain	This is the 2B and 2B-like sub-domain found in TraI (EC:5.99.1.2) a relaxase of F-family plasmids. It contains four domains; a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helica ...	This is the 2B and 2B-like sub-domain found in TraI (EC:5.99.1.2) a relaxase of F-family plasmids. It contains four domains; a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components. The 2B sub-domains in TraI are formed by residues 625-773 in the vestigial helicase domain and residues 1255-1397 in the active helicase domain. The 2B/2B-like sub-domain interacts with ssDNA where it contributes to the surface area where ssDNA bind. In other words the ssDNA-binding site is located in a groove between the 2B and 2B-like parts of the sub-domain. The sub-domain parts appear to act as clamps holding the ssDNA in place, resulting in the ssDNA being completely surrounded by protein. In previous studies, the 2B/2B-like sub-domain of the TraI vestigial helicase domain has been identified as translocation signal A (TSA) since it contains sequences essential for the recruitment of TraI to the T4S system. Thus, the 2B/2B-like sub-domain plays two major roles in relaxase function: (1) interacting with the DNA and possibly promoting high processivity and (2) mediating recruitment of the relaxosome to the T4S system [1].	Domain
H	PF08751	TrwC relaxase (TrwC)	TrwC relaxase	Relaxases are DNA strand transferases which function during the conjugative cell to cell DNA transfer. TrwC binds to the origin of transfer (oriT) and melts the double helix.	Domain
H	PF18272	single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)	single-stranded DNA binding TraI N-terminal subdomain	This is a subdomain found in TraI present in E. coli. Tra1 is a conjugative relaxase that forms part of the Type IV secretion system. This subdomain, referred to as 2A, is located in N-terminal region of the translocation signal (TSA) domain. TSA is ...	This is a subdomain found in TraI present in E. coli. Tra1 is a conjugative relaxase that forms part of the Type IV secretion system. This subdomain, referred to as 2A, is located in N-terminal region of the translocation signal (TSA) domain. TSA is known to reside in a larger ssDNA-binding domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	T-strand DNA (95-MER)	-	-	-
B	R-strand DNA (84-MER)	-	-	-
C	Integration host factor subunit alpha	DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity structural molecule activity structural constituent of chromatin	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process protein metabolic process regulation of metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process DNA recombination	bacterial nucleoid protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle IHF-DNA complex nucleoid DNA bending complex intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm cytosol
D	Integration host factor subunit beta	DNA binding binding nucleic acid binding structural molecule activity structural constituent of chromatin	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process 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 regulation of protein metabolic process translation post-transcriptional regulation of gene expression regulation of translation protein metabolic process DNA recombination	bacterial nucleoid protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle IHF-DNA complex nucleoid DNA bending complex intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome cytoplasm bacterial nucleoid protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle IHF-DNA complex nucleoid DNA bending complex intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome cytoplasm cytosol
E [auth F], F [auth E], G	Relaxosome protein TraY	DNA binding binding nucleic acid binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm
H	Multifunctional conjugation protein TraI	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 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 DNA binding nucleic acid binding nucleic acid conformation isomerase activity isomerase activity DNA topoisomerase type I (single strand cut, ATP-independent) activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity, acting on a nucleic acid catalytic activity macromolecular conformation isomerase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity helicase activity cation binding metal ion binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR010992	Integration host factor (IHF)-like DNA-binding domain superfamily	Homologous Superfamily
C	IPR020816	Histone-like DNA-binding protein, conserved site	Conserved Site
C	IPR005684	Integration host factor, alpha subunit	Family
C	IPR000119	Histone-like DNA-binding protein	Family
D	IPR010992	Integration host factor (IHF)-like DNA-binding domain superfamily	Homologous Superfamily
D	IPR020816	Histone-like DNA-binding protein, conserved site	Conserved Site
D	IPR005685	Integration host factor, beta subunit	Family
D	IPR000119	Histone-like DNA-binding protein	Family
E [auth F], F [auth E], G	IPR008876	Relaxosome protein TraY	Family
H	IPR014862	TrwC relaxase	Domain
H	IPR040987	TraI, N-terminal subdomain	Domain
H	IPR014059	TraI/TrwC, conjugative relaxase domain	Domain
H	IPR009767	DNA helicase, TraI type, C-terminal	Domain
H	IPR014129	Conjugative transfer relaxase protein TraI	Family
H	IPR040668	TraI, 2B/2B-like domain	Domain
H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
H	IPR054558	TraI, helicase-associated ssDBD, N-terminal	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.