4LJK | pdb_00004ljk

Structural insights into the unique single-stranded DNA binding mode of DNA processing protein A from Helicobacter pylori

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	LysR_substrate	e4ljkA1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: LysR_substrate	ECOD (v294.1)
B	LysR_substrate	e4ljkB1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: LysR_substrate	ECOD (v294.1)
C [auth E]	LysR_substrate	e4ljkE1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: LysR_substrate	ECOD (v294.1)
D [auth F]	LysR_substrate	e4ljkF1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: LysR_substrate	ECOD (v294.1)
E [auth H]	LysR_substrate	e4ljkH1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: LysR_substrate	ECOD (v294.1)
F [auth C]	LysR_substrate	e4ljkC1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: LysR_substrate	ECOD (v294.1)
G [auth D]	LysR_substrate	e4ljkD1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: LysR_substrate	ECOD (v294.1)
H [auth G]	LysR_substrate	e4ljkG1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: LysR_substrate	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C [auth E]	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D [auth F]	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E [auth H]	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F [auth C]	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
G [auth D]	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
H [auth G]	3.40.50.450	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, B, C [auth E], D [auth F], E [auth H], A, B, C [auth E], D [auth F], E [auth H], F [auth C], G [auth D], H [auth G]	PF02481	DNA recombination-mediator protein A (DNA_processg_A)	DNA recombination-mediator protein A	The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation [1]. It has now been shown that DprA is found to bind cooperatively to single-strand ...	The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation [1]. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth E], D [auth F], E [auth H], A, B, C [auth E], D [auth F], E [auth H], F [auth C], G [auth D], H [auth G]	DNA processing chain A (DprA)	DNA binding nucleic acid conformation isomerase activity isomerase activity binding single-stranded DNA binding catalytic activity, acting on a nucleic acid nucleic acid binding DNA/DNA annealing activity catalytic activity, acting on DNA annealing activity catalytic activity macromolecular conformation isomerase activity	DNA-mediated transformation horizontal gene transfer cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth E], D [auth F], E [auth H], A, B, C [auth E], D [auth F], E [auth H], F [auth C], G [auth D], H [auth G]	IPR057666	Smf/DprA, SLOG domain	Domain
A, B, C [auth E], D [auth F], E [auth H], A, B, C [auth E], D [auth F], E [auth H], F [auth C], G [auth D], H [auth G]	IPR003488	DNA recombination-mediator protein A	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.