1A04

THE STRUCTURE OF THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL IN THE MONOCLINIC C2 CRYSTAL FORM

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1a04a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	C-terminal effector domain of the bipartite response regulators	GerE-like (LuxR/UhpA family of transcriptional regulators)	Nitrate/nitrite response regulator (NarL)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1a04a2	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Nitrate/nitrite response regulator (NarL), receiver domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1a04b1	All alpha proteins	DNA/RNA-binding 3-helical bundle	C-terminal effector domain of the bipartite response regulators	GerE-like (LuxR/UhpA family of transcriptional regulators)	Nitrate/nitrite response regulator (NarL)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1a04b2	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Nitrate/nitrite response regulator (NarL), receiver domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	CheY-related	8031657	4003632	SCOP2 (2022-06-29)
A	SCOP2 Family	GerE-like (LuxR/UhpA family of transcriptional regulators)	8024262	4000720	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CheY-like	8044035	3001156	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C-terminal effector domain of the bipartite response regulators	8036641	3001179	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	CheY-like	8044035	3001156	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-terminal effector domain of the bipartite response regulators	8036641	3001179	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	GerE	e1a04A1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, LuxR-like	F: GerE	ECOD (1.6)
A	Response_reg	e1a04A2	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	GerE	e1a04B1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, LuxR-like	F: GerE	ECOD (1.6)
B	Response_reg	e1a04B2	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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	PF00196	Bacterial regulatory proteins, luxR family (GerE)	Bacterial regulatory proteins, luxR family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding 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 identical protein binding protein binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction cellular biosynthetic process RNA metabolic process regulation of primary metabolic process cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction 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 cellular metabolic process 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 regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process nitrate assimilation oxoacid metabolic process organic acid metabolic process reactive nitrogen species metabolic process nitrogen cycle metabolic process small molecule metabolic process nitrate metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR039420	Transcriptional regulatory protein WalR-like	Family
A, B	IPR011006	CheY-like superfamily	Homologous Superfamily
A, B	IPR001789	Signal transduction response regulator, receiver domain	Domain
A, B	IPR000792	Transcription regulator LuxR, C-terminal	Domain
A, B	IPR016032	Signal transduction response regulator, C-terminal effector	Homologous Superfamily
A, B	IPR036388	Winged helix-like 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.