Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilyRibosomal protein S5 domain 2-like 8037515 3000100 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyGHMP Kinase, C-terminal domain 8037516 3001245 SCOP2B (2022-06-29)
ASCOP2 FamilyGHMP Kinase, N-terminal domain 8025136 4000959 SCOP2 (2022-06-29)
ASCOP2 Family4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE 8025137 4000643 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyRibosomal protein S5 domain 2-like 8037515 3000100 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyGHMP Kinase, C-terminal domain 8037516 3001245 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BGHMP_kinases_Ne1oj4B2 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: GHMP_kinases_NECOD (1.6)
BUNK_F_TYPEe1oj4B1 A: a+b two layersX: Alpha-beta plaitsH: GHMP Kinase, C-terminal domain (From Topology)T: GHMP Kinase, C-terminal domainF: UNK_F_TYPEECOD (1.6)
AGHMP_kinases_Ne1oj4A2 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: GHMP_kinases_NECOD (1.6)
AUNK_F_TYPEe1oj4A1 A: a+b two layersX: Alpha-beta plaitsH: GHMP Kinase, C-terminal domain (From Topology)T: GHMP Kinase, C-terminal domainF: UNK_F_TYPEECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
B3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2CATH (4.3.0)
B3.30.70.890 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits GHMP kinase, C-terminal domainCATH (4.3.0)
A3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2CATH (4.3.0)
A3.30.70.890 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits GHMP kinase, C-terminal domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF08544GHMP kinases C terminal (GHMP_kinases_C)GHMP kinases C terminal- Family
A, B
PF00288GHMP kinases N terminal domain (GHMP_kinases_N)GHMP kinases N terminal domain- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE -

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

ChainsEnzyme NameDescriptionCatalytic Residues
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
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Explore in 3DM-CSA Motif Definition