7UV7

Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold duplex (21mer) containing the cognate REPE54 sequence and an insert duplex (10mer) with guest TAMRA-labelled thymine and T-A rich sequence.

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)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002854	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002855	3000034	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)
C	F_UNCLASSIFIED	e7uv7C1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF01051	Initiator Replication protein, WH1 (Rep3_N)	Initiator Replication protein, WH1	This protein is an initiator of plasmid replication [1-6]. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This entry also includes RepA which is ...	This protein is an initiator of plasmid replication [1-6]. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This entry also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene [3,4]. These proteins consist of two domains containing a winged helix-turn-helix motif, the N-terminal one, WH1, represented in this entry, is involved in the dimerization of RepE and an auxiliary binding to DNA. The C-terminal one, WH2, is related to a sequence-specific binding to the common 8 bp of the iteron [6].	Domain
C	PF21205	Initiator Rep protein, WH2 (Rep3_C)	Initiator Rep protein, WH2	This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E ...	This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene [1-3]. These proteins consist of two domains containing a winged helix-turn-helix motif: the N-terminal one, WH1, is involved in the dimerization of RepE and an auxiliary binding to DNA; the C-terminal one, WH2, represented in this entry, is related to a sequence-specific binding to the common 8 bp of the iteron [4,5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA (5'-D(APCPCPTPGPTPGPAPCPAPAPAPTPTPGPCPCPCPTPCP*A)-3')	-	-	-
B	DNA (5'-D(TPCPTPGPAPGPGPGPCPAPAPTPTPTPGPTPCPAPCPAP*G)-3')	-	-	-
C	Replication initiation protein	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding	cellular process plasmid maintenance nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-
D [auth E]	DNA (5'-D(GPAPCPGPGPTPAPAPTPT)-3')	-	-	-
E [auth F]	DNA (5'-D(GPT(TAMRA)PAPAPTPTPAPCPCPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR000525	Initiator Rep protein, WH1 domain	Domain
C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

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.