5JJV | pdb_00005jjv

Crystal structure of XerH site-specific recombinase bound to palindromic difH substrate: post-cleavage complex

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	Phage_integrase_C	e5jjvA2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_C	ECOD (1.6)
A	Phage_integrase_N	e5jjvA1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_N	ECOD (1.6)
A	EUF07959	e5jjvA3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: EUF07959	ECOD (1.6)
B	Phage_integrase_C	e5jjvB1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_C	ECOD (1.6)
B	Phage_integrase_N	e5jjvB2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_N	ECOD (1.6)
B	EUF07959	e5jjvB3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: EUF07959	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.443.10	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (utative)
B	1.10.443.10	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00589	Phage integrase family (Phage_integrase)	Phage integrase family	-	Family
A, B	PF18644	Phage integrase SAM-like domain (Phage_int_SAM_6)	Phage integrase SAM-like domain	Xer recombinases are members of the tyrosine site-specific recombinase superfamily, a large group of enzymes that catalyze DNA breakage and rejoining using a conserved tyrosine nucleophile. Tyrosine recombinases promote various programmed DNA rearran ...	Xer recombinases are members of the tyrosine site-specific recombinase superfamily, a large group of enzymes that catalyze DNA breakage and rejoining using a conserved tyrosine nucleophile. Tyrosine recombinases promote various programmed DNA rearrangements including the monomerization of phage, plasmid and chromosome multimers, resolution of hairpin telomeres, and the movement of virulence and antibiotic resistance carrying integrative mobile genetic elements. Structural analysis of Helicobacter pylori XerH indicates that this N-terminal domain consisting of six alpha-helices contacts the DNA using a four-helix bundle [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Tyrosine recombinase XerH	DNA binding binding nucleic acid binding tyrosine-based site-specific recombinase activity integrase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity site-specific recombinase activity	cellular process cell division cell cycle chromosome segregation cell cycle process nucleobase-containing compound metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
C, E	DNA (5'-D(TPAPGPTPTPAPTPGPAPAPAPAP*C)-3')	-	-	-
D, F	DNA (5'-D(TPGPCPAPGPTPTPTPTPCPAPTPAPAPCPTP*A)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011010	DNA breaking-rejoining enzyme, catalytic core	Homologous Superfamily
A, B	IPR050090	Bacterial tyrosine recombinase XerC/XerD complex	Family
A, B	IPR033683	Tyrosine recombinase XerH	Family
A, B	IPR041308	Xer recombinase, N-terminal	Domain
A, B	IPR044068	Core-binding (CB) domain	Domain
A, B	IPR002104	Integrase, catalytic domain	Domain
A, B	IPR013762	Integrase-like, catalytic 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.