3JA6

Cryo-electron Tomography and All-atom Molecular Dynamics Simulations Reveal a Novel Kinase Conformational Switch in Bacterial Chemotaxis Signaling

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	SCOP2B Superfamily	CheW-like	8038860	3000623	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CheW-like	8038860	3000623	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CheW-like	8038860	3000623	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	CheW-like	8038860	3000623	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CheW-like	8041990	3000623	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homodimeric domain of signal transducing histidine kinase	8037206	3001864	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GHKL (Gyrase Hsp90 Histidine Kinase MutL) domain-like	8033664	3000091	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GHKL (Gyrase Hsp90 Histidine Kinase MutL) domain-like	8033664	3000091	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	CheW-like	8041990	3000623	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Homodimeric domain of signal transducing histidine kinase	8037206	3001864	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Methyl-accepting chemotaxis protein (MCP) signaling domain	8038876	3001685	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	PF01584	e3ja6A2	A: beta barrels	X: OB-fold	H: CheW (From Topology)	T: CheW	F: PF01584	ECOD (1.6)
B	PF01584	e3ja6B2	A: beta barrels	X: OB-fold	H: CheW (From Topology)	T: CheW	F: PF01584	ECOD (1.6)
D	PF01584	e3ja6D1	A: beta barrels	X: OB-fold	H: CheW (From Topology)	T: CheW	F: PF01584	ECOD (1.6)
F	PF01584	e3ja6F2	A: beta barrels	X: OB-fold	H: CheW (From Topology)	T: CheW	F: PF01584	ECOD (1.6)
C	PF01584	e3ja6C1	A: beta barrels	X: OB-fold	H: CheW (From Topology)	T: CheW	F: PF01584	ECOD (1.6)
C	PF02895	e3ja6C3	A: alpha duplicates or obligate multimers	X: ROP-like	H: Homodimeric domain of signal transducing histidine kinase (From Topology)	T: Homodimeric domain of signal transducing histidine kinase	F: PF02895	ECOD (1.6)
C	PF02518	e3ja6C2	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: PF02518	ECOD (1.6)
E	PF01584	e3ja6E4	A: beta barrels	X: OB-fold	H: CheW (From Topology)	T: CheW	F: PF01584	ECOD (1.6)
E	PF02895	e3ja6E3	A: alpha duplicates or obligate multimers	X: ROP-like	H: Homodimeric domain of signal transducing histidine kinase (From Topology)	T: Homodimeric domain of signal transducing histidine kinase	F: PF02895	ECOD (1.6)
E	PF02518	e3ja6E1	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: PF02518	ECOD (1.6)
H	PF00015	e3ja6H1	A: alpha bundles	X: Long alpha-hairpin	H: GreA transcript cleavage protein, N-terminal domain (From Topology)	T: GreA transcript cleavage protein, N-terminal domain	F: PF00015	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, D, F	PF01584	CheW-like domain (CheW)	CheW-like domain	CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related pr ...	CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis. The CheW-like regulatory domain in CheA [1] binds to CheW, suggesting that these domains can interact with each other.	Domain
C, E	PF02518	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (HATPase_c)	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.	Domain
C, E	PF01584	CheW-like domain (CheW)	CheW-like domain	CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related pr ...	CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis. The CheW-like regulatory domain in CheA [1] binds to CheW, suggesting that these domains can interact with each other.	Domain
C, E	PF02895	Signal transducing histidine kinase, homodimeric domain (H-kinase_dim)	Signal transducing histidine kinase, homodimeric domain	This helical bundle domain is the homodimer interface of the signal transducing histidine kinase family.	Domain
G, I, K, M, O G, I, K, M, O, Q	PF00015	Methyl-accepting chemotaxis protein (MCP) signalling domain (MCPsignal)	Methyl-accepting chemotaxis protein (MCP) signalling domain	-	Family
H, J, L, N, P H, J, L, N, P, R	PF00015	Methyl-accepting chemotaxis protein (MCP) signalling domain (MCPsignal)	Methyl-accepting chemotaxis protein (MCP) signalling domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, D, F	Chemotaxis protein CheW	protein binding binding protein domain specific binding	chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation cellular process signal transduction cell communication	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
C, E	Chemotaxis protein CheA	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 protein binding protein domain specific binding catalytic activity, acting on a protein 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 catalytic activity	chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion	intracellular anatomical structure cytoplasm cellular anatomical entity
G, I, K, M, O G, I, K, M, O, Q	Methyl-accepting chemotaxis protein 2	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation cellular process signal transduction cell communication	cell periphery plasma membrane membrane cellular anatomical entity
H, J, L, N, P H, J, L, N, P, R	Methyl-accepting chemotaxis protein 2	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation cellular process signal transduction cell communication	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, D, F	IPR039315	Chemotaxis protein CheW	Family
A, B, D, F	IPR002545	CheW-like domain	Domain
A, B, D, F	IPR036061	CheW-like domain superfamily	Homologous Superfamily
C, E	IPR037006	Histidine kinase CheA-like, homodimeric domain superfamily	Homologous Superfamily
C, E	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Domain
C, E	IPR004105	Histidine kinase CheA-like, homodimeric domain	Domain
C, E	IPR003594	Histidine kinase/HSP90-like ATPase	Domain
C, E	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily	Homologous Superfamily
C, E	IPR036061	CheW-like domain superfamily	Homologous Superfamily
C, E	IPR037052	Chemotaxis protein CheA, P2 response regulator-binding domain superfamily	Homologous Superfamily
C, E	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
C, E	IPR010808	Chemotaxis protein CheA, P2 response regulator-binding	Domain
C, E	IPR002545	CheW-like domain	Domain
C, E	IPR005467	Histidine kinase domain	Domain
C, E	IPR036641	HPT domain superfamily	Homologous Superfamily
C, E	IPR008207	Signal transduction histidine kinase, phosphotransfer (Hpt) domain	Domain
C, E	IPR035891	CheY-binding domain of CheA	Homologous Superfamily
G, I, K, M, O G, I, K, M, O, Q	IPR000727	Target SNARE coiled-coil homology domain	Domain
G, I, K, M, O G, I, K, M, O, Q	IPR004090	Chemotaxis methyl-accepting receptor	Family
G, I, K, M, O G, I, K, M, O, Q	IPR004089	Methyl-accepting chemotaxis protein (MCP) signalling domain	Domain
H, J, L, N, P H, J, L, N, P, R	IPR000727	Target SNARE coiled-coil homology domain	Domain
H, J, L, N, P H, J, L, N, P, R	IPR004090	Chemotaxis methyl-accepting receptor	Family
H, J, L, N, P H, J, L, N, P, R	IPR004089	Methyl-accepting chemotaxis protein (MCP) signalling domain	Domain