1X9J

Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes

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	d1x9ja1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetokinase-like	butyrate kinase 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1x9jb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetokinase-like	butyrate kinase 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C	d1x9jc1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetokinase-like	butyrate kinase 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
D	d1x9jd1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetokinase-like	butyrate kinase 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
E	d1x9je1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetokinase-like	butyrate kinase 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
F	d1x9jf1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetokinase-like	butyrate kinase 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
G	d1x9jg1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetokinase-like	butyrate kinase 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
H	d1x9jh1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetokinase-like	butyrate kinase 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Actin-like ATPases	8032377	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8032376	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8032377	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8032376	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8032376	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8032377	3000092	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Actin-like ATPases	8032377	3000092	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Actin-like ATPases	8032376	3000092	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Actin-like ATPases	8032377	3000092	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Actin-like ATPases	8032376	3000092	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Actin-like ATPases	8032376	3000092	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Actin-like ATPases	8032377	3000092	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Actin-like ATPases	8032377	3000092	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Actin-like ATPases	8032376	3000092	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Actin-like ATPases	8032376	3000092	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Actin-like ATPases	8032377	3000092	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	Acetate_kinase_C	e1x9jA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_C	ECOD (1.6)
A	Acetate_kinase_N	e1x9jA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_N	ECOD (1.6)
B	Acetate_kinase_C	e1x9jB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_C	ECOD (1.6)
B	Acetate_kinase_N	e1x9jB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_N	ECOD (1.6)
C	Acetate_kinase_C	e1x9jC2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_C	ECOD (1.6)
C	Acetate_kinase_N	e1x9jC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_N	ECOD (1.6)
D	Acetate_kinase_C	e1x9jD2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_C	ECOD (1.6)
D	Acetate_kinase_N	e1x9jD1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_N	ECOD (1.6)
E	Acetate_kinase_C	e1x9jE2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_C	ECOD (1.6)
E	Acetate_kinase_N	e1x9jE1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_N	ECOD (1.6)
F	Acetate_kinase_C	e1x9jF2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_C	ECOD (1.6)
F	Acetate_kinase_N	e1x9jF1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_N	ECOD (1.6)
G	Acetate_kinase_C	e1x9jG2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_C	ECOD (1.6)
G	Acetate_kinase_N	e1x9jG1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_N	ECOD (1.6)
H	Acetate_kinase_C	e1x9jH2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_C	ECOD (1.6)
H	Acetate_kinase_N	e1x9jH1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Acetate_kinase_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
G	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
H	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00871	Acetokinase family (Acetate_kinase)	Acetokinase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Probable butyrate kinase 2	kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity acetate kinase activity transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity acetate kinase activity transferase activity, transferring phosphorus-containing groups 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 butyrate kinase activity	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic substance metabolic process oxoacid metabolic process carboxylic acid metabolic process acetate metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000890	Aliphatic acid kinase, short-chain	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011245	Butyrate kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023865	Aliphatic acid kinase, short-chain, conserved site	Conserved Site

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.