3EZI

Crystal Structure of the E. coli Histidine Kinase NarX Sensor Domain without Ligand

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	SCOP2 Family	Histidine kinase NarX sensory domain - like	8018628	4004018	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Chemoreceptors ligand-binding domain	8018629	3001511	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Chemoreceptors ligand-binding domain	8018629	3001511	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Chemoreceptors ligand-binding domain	8018629	3001511	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Chemoreceptors ligand-binding domain	8018629	3001511	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	PF13675	e3eziA1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Histidine kinase associated sensor domains (From Topology)	T: Histidine kinase associated sensor domains	F: PF13675	ECOD (1.6)
B	PF13675	e3eziB1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Histidine kinase associated sensor domains (From Topology)	T: Histidine kinase associated sensor domains	F: PF13675	ECOD (1.6)
C	PF13675	e3eziC1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Histidine kinase associated sensor domains (From Topology)	T: Histidine kinase associated sensor domains	F: PF13675	ECOD (1.6)
D	PF13675	e3eziD1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Histidine kinase associated sensor domains (From Topology)	T: Histidine kinase associated sensor domains	F: PF13675	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.960	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Histidine kinase NarX, sensor domain	CATH (4.3.0)
B	1.20.120.960	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Histidine kinase NarX, sensor domain	CATH (4.3.0)
C	1.20.120.960	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Histidine kinase NarX, sensor domain	CATH (4.3.0)
D	1.20.120.960	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Histidine kinase NarX, sensor domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13675	Type IV pili methyl-accepting chemotaxis transducer N-term (PilJ)	Type IV pili methyl-accepting chemotaxis transducer N-term	This domain is found on many type IV pili methyl-accepting chemotaxis transducer proteins [1] where there is also a HAMP signature towards the C-terminus. It is a monomodular four-helix bundle and recognises nitrate and nitrite (Matilla et al. FEMS ...	This domain is found on many type IV pili methyl-accepting chemotaxis transducer proteins [1] where there is also a HAMP signature towards the C-terminus. It is a monomodular four-helix bundle and recognises nitrate and nitrite (Matilla et al. FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Nitrate/nitrite sensor protein narX	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 identical protein binding protein binding protein homodimerization activity protein dimerization activity phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity small molecule sensor activity kinase activity protein kinase activity transferase activity phosphotransferase activity, nitrogenous group as acceptor phosphotransferase activity, alcohol group as acceptor protein histidine kinase activity transferase activity, transferring phosphorus-containing groups phosphorelay sensor kinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular response to nitrogen compound cellular response to inorganic substance response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to inorganic substance cellular response to chemical stimulus response to nitrate cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular response to nitrogen compound cellular response to inorganic substance response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to inorganic substance cellular response to chemical stimulus response to nitrate response to chemical cellular response to nitrate cellular response to reactive nitrogen species response to nitrite cellular response to nitrite nitrate assimilation oxoacid metabolic process cellular metabolic process organic acid metabolic process reactive nitrogen species metabolic process nitrogen cycle metabolic process organic substance metabolic process metabolic process small molecule metabolic process nitrate metabolic process regulation of biological process regulation of cellular process signaling biological regulation signal transduction cell communication	cell periphery plasma membrane membrane cellular anatomical entity outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029095	NarX-like, N-terminal	Domain
A, B, C, D	IPR003594	Histidine kinase/HSP90-like ATPase	Domain
A, B, C, D	IPR003660	HAMP domain	Domain
A, B, C, D	IPR011712	Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain	Domain
A, B, C, D	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B, C, D	IPR005467	Histidine kinase domain	Domain
A, B, C, D	IPR042295	NarX-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR016380	Signal transduction histidine kinase, nitrate/nitrite-sensing	Family

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.