1OJ4

Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1oj4a1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
A	d1oj4a2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
B	d1oj4b1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
B	d1oj4b2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GHMP Kinase, N-terminal domain	8025136	4000959	SCOP2 (2022-06-29)
A	SCOP2 Family	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE	8025137	4000643	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosomal protein S5 domain 2-like	8037515	3000100	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GHMP Kinase, C-terminal domain	8037516	3001245	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8037515	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8037516	3001245	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	GHMP_kinases_N	e1oj4A2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: GHMP_kinases_N	ECOD (1.6)
A	UNK_F_TYPE	e1oj4A1	A: a+b two layers	X: Alpha-beta plaits	H: GHMP Kinase, C-terminal domain (From Topology)	T: GHMP Kinase, C-terminal domain	F: UNK_F_TYPE	ECOD (1.6)
B	GHMP_kinases_N	e1oj4B2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: GHMP_kinases_N	ECOD (1.6)
B	UNK_F_TYPE	e1oj4B1	A: a+b two layers	X: Alpha-beta plaits	H: GHMP Kinase, C-terminal domain (From Topology)	T: GHMP Kinase, C-terminal domain	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
A	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)
B	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
B	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08544	GHMP kinases C terminal (GHMP_kinases_C)	GHMP kinases C terminal	-	Family
A, B	PF00288	GHMP kinases N terminal domain (GHMP_kinases_N)	GHMP kinases N terminal domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE	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 kinase activity transferase activity 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process terpenoid biosynthetic process terpenoid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006204	GHMP kinase N-terminal domain	Domain
A, B	IPR013750	GHMP kinase, C-terminal domain	Domain
A, B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B	IPR004424	4-diphosphocytidyl-2C-methyl-D-erythritol kinase	Family
A, B	IPR036554	GHMP kinase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase M-CSA #654	4-(cytidine 5'-diphospho0-2-C-methyl-D-erythritol (CDP-ME) kinase catalyses phosphorylation of the 2-hydroxyl group of CDP-ME, the fourth step of the dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) biosynthesis pathways. IPP and DMAPP are universal precursors of isoprenoids, an important family of natural products, such as sterols, dilichols, triterpernes and ubiquinones and thus contribute to many biological functions. Two biosynthetic routes to IPP and DMAPP have evolved. Eukaryotes, archaebacteria and a few eubacteria uses the mevalonate pathway but in most eubacteria, algae, chloroplasts and cyanobacteria, the 1-deoxy-D-xylulose-5-phosphate (DOXP) pathway is used. The bacteria using DOXP pathway include some that cause serious human diseases and since the enzymes in DOXP pathway have no ortholog in human, they are the target for structure-based antimicrobial drug development.	Defined by 2 residues: LYS:A-10ASP:A-141 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.1.148 (PDB Primary Data) Search M-CSA Motif + EC 2.7.1.148

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.