1OJ4
Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
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) |
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) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
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) |
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) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
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) |
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) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF08544 | GHMP kinases C terminal (GHMP_kinases_C) | GHMP kinases C terminal | - | Family | |
PF00288 | GHMP kinases N terminal domain (GHMP_kinases_N) | GHMP kinases N terminal domain | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR006204 | GHMP kinase N-terminal domain | Domain | |
IPR013750 | GHMP kinase, C-terminal domain | Domain | |
IPR020568 | Ribosomal protein uS5 domain 2-type superfamily | Homologous Superfamily | |
IPR004424 | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase | Family | |
IPR036554 | GHMP kinase, C-terminal domain superfamily | Homologous Superfamily | |
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 |
---|---|---|---|
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. | EC: 2.7.1.148 (PDB Primary Data) |