2BON | pdb_00002bon

Structure of an Escherichia coli lipid kinase (YegS)

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	d2bona1	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	Diacylglycerol kinase-like	Lipid kinase YegS	ESCHERICHIA COLI (Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
A	d2bona2	Artifacts	Tags	Tags	Tags	C-terminal Tags	ESCHERICHIA COLI (Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
B	d2bonb2	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	Diacylglycerol kinase-like	Lipid kinase YegS	ESCHERICHIA COLI (Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
B	d2bonb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	ESCHERICHIA COLI (Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Diacylglycerol kinase-like	8021181	4002740	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NAD kinase/diacylglycerol kinase-like	8033561	3001940	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	NAD kinase/diacylglycerol kinase-like	8033561	3001940	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	PRK13054	e2bonA1	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: PRK13054	ECOD (1.6)
A	DAGK_cat	e2bonA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: DAGK_cat	ECOD (1.6)
B	PRK13054	e2bonB2	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: PRK13054	ECOD (1.6)
B	DAGK_cat	e2bonB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: DAGK_cat	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
A	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
B	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
B	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF19279	YegS C-terminal NAD kinase beta sandwich-like domain (YegS_C)	YegS C-terminal NAD kinase beta sandwich-like domain	This entry represents the C-terminal domain found in the YegS protein [1,2]. It is related to the beta sandwich domain of NAD kinases. The structure of YegS reveals a two-domain protein with the active site crevice found between the two domains. The ...	This entry represents the C-terminal domain found in the YegS protein [1,2]. It is related to the beta sandwich domain of NAD kinases. The structure of YegS reveals a two-domain protein with the active site crevice found between the two domains. The C-terminal domain contains 13 beta-strands and two alpha-helices. The likely substrate for YegS is phosphatidylglycerol [1].	Domain
A, B	PF00781	Diacylglycerol kinase catalytic domain (DAGK_cat)	Diacylglycerol kinase catalytic domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	LIPID KINASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding kinase activity lipid kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	membrane lipid metabolic process sphingolipid metabolic process primary metabolic process metabolic process cellular process lipid metabolic process lipid biosynthetic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process	cellular anatomical structure membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045540	YegS/DAGK, C-terminal domain	Domain
A, B	IPR017438	Inorganic polyphosphate/ATP-NAD kinase, N-terminal	Homologous Superfamily
A, B	IPR001206	Diacylglycerol kinase, catalytic domain	Domain
A, B	IPR022433	Lipid kinase YegS	Family
A, B	IPR050187	Lipid Phosphate Formation and Regulation	Family
A, B	IPR016064	NAD kinase/diacylglycerol kinase-like domain superfamily	Homologous Superfamily
A, B	IPR005218	Diacylglycerol/lipid kinase	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 R01GM157729.