2IEF

Structure of the cooperative Excisionase (Xis)-DNA complex reveals a micronucleoprotein filament

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)
D [auth A]	d2iefa_	All alpha proteins	Putative DNA-binding domain	Putative DNA-binding domain	Excisionase-like	Excisionase Xis	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
E [auth B]	d2iefb_	All alpha proteins	Putative DNA-binding domain	Putative DNA-binding domain	Excisionase-like	Excisionase Xis	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
F [auth C]	d2iefc_	All alpha proteins	Putative DNA-binding domain	Putative DNA-binding domain	Excisionase-like	Excisionase Xis	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2B Superfamily	Putative DNA-binding domain	8038870	3000158	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Putative DNA-binding domain	8038870	3000158	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Putative DNA-binding domain	8038870	3000158	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)
D [auth A]	Exc	e2iefA1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: Exc	ECOD (1.6)
E [auth B]	Exc	e2iefB1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: Exc	ECOD (1.6)
F [auth C]	Exc	e2iefC1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: Exc	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	1.10.1660.20	Mainly Alpha	Orthogonal Bundle	Multidrug-efflux Transporter Regulator	Chain: A	CATH (4.3.0)
E [auth B]	1.10.1660.20	Mainly Alpha	Orthogonal Bundle	Multidrug-efflux Transporter Regulator	Chain: A	CATH (4.3.0)
F [auth C]	1.10.1660.20	Mainly Alpha	Orthogonal Bundle	Multidrug-efflux Transporter Regulator	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A], E [auth B], F [auth C]	PF07825	Excisionase-like protein (Exc)	Excisionase-like protein	The phage-encoded excisionase protein (Xis, Swiss:P03699) is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual 'winged'-helix structure in which two alpha ...	The phage-encoded excisionase protein (Xis, Swiss:P03699) is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual 'winged'-helix structure in which two alpha helices are packed against two extended strands. Also present in the structure is a two-stranded anti-parallel beta-sheet, whose strands are connected by a four-residue 'wing'. During interaction with DNA, helix alpha2 is thought to insert into the major groove, while the wing contacts the adjacent minor groove or phosphodiester backbone. The C-terminal region of Xis is involved in interaction with phage-encoded integrase (Int), and a putative C-terminal alpha helix may fold upon interaction with Int and/or DNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D]	15-mer DNA	-	-	-
B [auth E]	19-mer DNA	-	-	-
C [auth F]	34-mer DNA	-	-	-
D [auth A], E [auth B], F [auth C]	Excisionase	DNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process provirus excision latent virus replication viral latency viral process release from viral latency	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A], E [auth B], F [auth C]	IPR012884	Excisionase-like	Domain
D [auth A], E [auth B], F [auth C]	IPR038137	Excisionase-like superfamily	Homologous Superfamily
D [auth A], E [auth B], F [auth C]	IPR009061	Putative DNA-binding domain superfamily	Homologous Superfamily

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.