5ED4 | pdb_00005ed4

Structure of a PhoP-DNA 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)
F	Trans_reg_C	e5ed4F1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Trans_reg_C	ECOD (1.6)
F	Response_reg	e5ed4F2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)
E	Trans_reg_C	e5ed4E1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Trans_reg_C	ECOD (1.6)
E	Response_reg	e5ed4E2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)
B	Trans_reg_C	e5ed4B2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Trans_reg_C	ECOD (1.6)
B	Response_reg	e5ed4B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)
A	Trans_reg_C	e5ed4A2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Trans_reg_C	ECOD (1.6)
A	Response_reg	e5ed4A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
F	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
E	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E, F	PF00072	Response regulator receiver domain (Response_reg)	Response regulator receiver domain	This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Domain
A, B, E, F	PF00486	Transcriptional regulatory protein, C terminal (Trans_reg_C)	Transcriptional regulatory protein, C terminal		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H	DNA (26-MER)	-	-	-
C, G	DNA (26-MER)	-	-	-
A, B, E, F	Response regulator	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding molecular transducer activity phosphorelay response regulator activity cation binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process membrane lipid metabolic process carbohydrate derivative biosynthetic process glycolipid metabolic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process glycolipid biosynthetic process membrane lipid biosynthetic process lipid metabolic process establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein secretion by the type VII secretion system protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport macromolecule localization intracellular protein localization positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of DNA-templated transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process response to oxidative stress response to stimulus response to stress regulation of lipid metabolic process positive regulation of lipid biosynthetic process positive regulation of lipid metabolic process regulation of lipid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E, F	IPR039420	Transcriptional regulatory protein WalR-like	Family
A, B, E, F	IPR001867	OmpR/PhoB-type DNA-binding domain	Domain
A, B, E, F	IPR011006	CheY-like superfamily	Homologous Superfamily
A, B, E, F	IPR001789	Signal transduction response regulator, receiver domain	Domain
A, B, E, F	IPR016032	Signal transduction response regulator, C-terminal effector	Homologous Superfamily
A, B, E, F	IPR036388	Winged helix-like 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.