3EZW | pdb_00003ezw

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3ezwa1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Glycerol kinase	Glycerol kinase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3ezwb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Glycerol kinase	Glycerol kinase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth E]	d3ezwe1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Glycerol kinase	Glycerol kinase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D [auth G]	d3ezwg1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Glycerol kinase	Glycerol kinase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E [auth C]	d3ezwc1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Glycerol kinase	Glycerol kinase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F [auth D]	d3ezwd1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Glycerol kinase	Glycerol kinase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G [auth F]	d3ezwf1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Glycerol kinase	Glycerol kinase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
H	d3ezwh1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Glycerol kinase	Glycerol kinase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Glycerol kinase	8031382	4000532	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8043760	3000092	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8043761	3000092	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8043761	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8043760	3000092	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Actin-like ATPases	8043761	3000092	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Actin-like ATPases	8043760	3000092	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Actin-like ATPases	8043760	3000092	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Actin-like ATPases	8043761	3000092	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Actin-like ATPases	8043761	3000092	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Actin-like ATPases	8043760	3000092	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Actin-like ATPases	8043760	3000092	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Actin-like ATPases	8043761	3000092	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Actin-like ATPases	8043760	3000092	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Actin-like ATPases	8043761	3000092	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Actin-like ATPases	8043760	3000092	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Actin-like ATPases	8043761	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		e3ezwA1	A: Insertion domain in tetravirus coat protein	X: Insertion domain in tetravirus coat protein	H: Insertion domain in tetravirus coat protein	T: FGGY_C	F:	ECOD (20:10:01)
B		e3ezwB1	A: HTH	X: HTH	H: winged helix domain	T: Peripla_BP_3	F:	ECOD (20:10:01)
C [auth E]		e3ezwE1	A: HTH	X: HTH	H: winged helix domain	T: Peripla_BP_3	F:	ECOD (20:10:01)
D [auth G]		e3ezwG1	A: HTH	X: HTH	H: winged helix domain	T: Peripla_BP_3	F:	ECOD (20:10:01)
E [auth C]		e3ezwC1	A: HTH	X: HTH	H: winged helix domain	T: Peripla_BP_3	F:	ECOD (20:10:01)
F [auth D]		e3ezwD1	A: HTH	X: HTH	H: winged helix domain	T: Peripla_BP_3	F:	ECOD (20:10:01)
G [auth F]		e3ezwF1	A: HTH	X: HTH	H: winged helix domain	T: Peripla_BP_3	F:	ECOD (20:10:01)
H		e3ezwH1	A: HTH	X: HTH	H: winged helix domain	T: Peripla_BP_3	F:	ECOD (20:10:01)

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 [auth E]	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D [auth G]	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E [auth C]	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F [auth D]	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
G [auth F]	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 [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	PF00370	FGGY family of carbohydrate kinases, N-terminal domain (FGGY_N)	FGGY family of carbohydrate kinases, N-terminal domain	This domain adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain.	Domain
A, B, C [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	PF02782	FGGY family of carbohydrate kinases, C-terminal domain (FGGY_C)	FGGY family of carbohydrate kinases, C-terminal domain	This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	Glycerol kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase activity glycerol kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding metal ion binding identical protein binding protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process carbohydrate metabolic process polyol metabolic process alcohol catabolic process catabolic process polyol catabolic process carbohydrate catabolic process primary metabolic process alcohol metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process carbohydrate metabolic process polyol metabolic process alcohol catabolic process catabolic process polyol catabolic process carbohydrate catabolic process primary metabolic process alcohol metabolic process alditol catabolic process glycerol metabolic process glycerol catabolic process metabolic process small molecule metabolic process small molecule catabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process phosphate-containing compound metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process phosphorus metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	IPR018483	Carbohydrate kinase, FGGY, conserved site	Conserved Site
A, B, C [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B, C [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	IPR018485	Carbohydrate kinase FGGY, C-terminal	Domain
A, B, C [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	IPR005999	Glycerol kinase	Family
A, B, C [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	IPR000577	Carbohydrate kinase, FGGY	Family
A, B, C [auth E], D [auth G], E [auth C], A, B, C [auth E], D [auth G], E [auth C], F [auth D], G [auth F], H	IPR018484	Carbohydrate kinase FGGY, N-terminal	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.