6P0T

Crystal structure of ternary DNA complex "FX(1-2)-1Xis" containing E. coli Fis and phage lambda Xis

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Homeodomain-like	8002272	3000001	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Homeodomain-like	8002272	3000001	SCOP2B (2022-06-29)
E	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)
A [auth B]	PF02954	e6p0tB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF02954	ECOD (1.6)
B [auth A]	PF02954	e6p0tA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF02954	ECOD (1.6)
E	PF07825	e6p0tE1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: PF07825	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (utative)
B [auth A]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (utative)
E	1.10.1660.20	Mainly Alpha	Orthogonal Bundle	Multidrug-efflux Transporter Regulator	Chain: A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A]	PF02954	Bacterial regulatory protein, Fis family (HTH_8)	Bacterial regulatory protein, Fis family	-	Domain
E	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
C	DNA (27-MER), FX1-2	-	-	-
D	DNA (27-MER), FX1-2	-	-	-
A [auth B], B [auth A]	DNA-binding protein Fis	DNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity 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 DNA binding, bending DNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity 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 DNA binding, bending sequence-specific DNA binding, bending core promoter sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity DNA-binding transcription repressor activity	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process regulation of DNA recombination positive regulation of biological process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of DNA recombination positive regulation of nucleobase-containing compound metabolic process DNA recombination DNA metabolic process positive regulation of DNA metabolic process regulation of DNA metabolic process cellular component organization organelle organization chromosome organization cellular component organization or biogenesis response to stimulus response to radiation response to abiotic stimulus provirus excision latent virus replication viral latency viral process release from viral latency	protein-containing complex catalytic complex invertasome intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-DNA complex nucleosome chromatin chromosome intracellular organelle organelle protein-containing complex catalytic complex invertasome intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-DNA complex nucleosome chromatin chromosome intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleoid
E	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
A [auth B], B [auth A]	IPR002197	DNA binding HTH domain, Fis-type	Domain
A [auth B], B [auth A]	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR005412	DNA-binding protein Fis	Family
E	IPR012884	Excisionase-like	Domain
E	IPR038137	Excisionase-like superfamily	Homologous Superfamily
E	IPR009061	Putative 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 R01GM133198.