HAMAP rule MF_01520
General rule information
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Accession | MF_01520 |
Dates | 13-AUG-2004 (Created) 1-JUN-2023 (Last updated, Version 35) |
Name | IspDF |
Scope | Bacteria |
Templates | Q9PM68 (ISPDF_CAMJE); Q46893 (ISPD_ECOLI); P62617 (ISPF_ECOLI): [Recover all] |
Triggered by |
Propagated annotation
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Identifier, protein and gene names
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Identifier |
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Protein name |
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Gene name |
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Comments
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Function | Bifunctional enzyme that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP) (IspD), and catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (IspF). |
Catalytic activity | RHEA:13429: 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate
EC 2.7.7.60 |
RHEA:23864: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP
EC 4.6.1.12 |
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Cofactor | a divalent metal cation |
Pathway | Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. |
Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6. | |
Similarity | In the N-terminal section; belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. |
In the C-terminal section; belongs to the IspF family. |
Keywords
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Gene Ontology
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GO:0008685; Molecular function: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity.
GO:0050518; Molecular function: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity.
GO:0016114; Biological process: terpenoid biosynthetic process.
GO:0050518; Molecular function: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity.
GO:0016114; Biological process: terpenoid biosynthetic process.
Cross-references
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Pfam | PF01128; IspD; 1; |
PF02542; YgbB; 1; | |
NCBIfam | TIGR00453; IspD; 1; |
TIGR00151; IspF; 1; | |
PROSITE | PS01295; ISPD; 1; |
PS01350; ISPF; 1; |
Features
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From: ISPDF_CAMJE (Q9PM68) | ||||||||||||
Key | From | To | Description | Tag | Condition | FTGroup | ||||||
REGION | Nter | 210 | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | |||||||||
REGION | 211 | Cter | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | |||||||||
BINDING | 217 | 219 | /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" /ligand_id="ChEBI:CHEBI:57919 | D-x-H | ||||||||
BINDING | 243 | 244 | /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" /ligand_id="ChEBI:CHEBI:57919 | H-S | ||||||||
BINDING | 265 | 267 | /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" /ligand_id="ChEBI:CHEBI:57919 | D-[IL]-G | ||||||||
BINDING | 270 | 274 | /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" /ligand_id="ChEBI:CHEBI:57919 | [FY]-x-D-x-[DNE] | ||||||||
BINDING | 309 | 315 | /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" /ligand_id="ChEBI:CHEBI:57919 | [AL]-x(2)-P-[KR]-M-[LAG] | ||||||||
BINDING | 341 | 344 | /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" /ligand_id="ChEBI:CHEBI:57919 | [TS]-[T]-x-[ED] | ||||||||
BINDING | 217 | 217 | /ligand="a divalent metal cation" /ligand_id="ChEBI:CHEBI:60240 | D | ||||||||
BINDING | 219 | 219 | /ligand="a divalent metal cation" /ligand_id="ChEBI:CHEBI:60240 | H | ||||||||
BINDING | 251 | 251 | /ligand="a divalent metal cation" /ligand_id="ChEBI:CHEBI:60240 | H | ||||||||
BINDING | 348 | 348 | /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" /ligand_id="ChEBI:CHEBI:57919 | [FY] | ||||||||
BINDING | 351 | 351 | /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" /ligand_id="ChEBI:CHEBI:57919 | [RK] | ||||||||
SITE | 16 | 16 | Transition state stabilizer | R | ||||||||
SITE | 23 | 23 | Transition state stabilizer | K | ||||||||
SITE | 139 | 139 | Positions MEP for the nucleophilic attack | [RH] | ||||||||
SITE | 191 | 191 | Positions MEP for the nucleophilic attack | K | ||||||||
SITE | 243 | 243 | Transition state stabilizer | [HDN] | ||||||||
SITE | 342 | 342 | Transition state stabilizer | [TS] |
Additional information
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Size range | 359-422 amino acids |
Related rules | MF_00107 (ISPF); MF_00108 (ISPD) |
Fusion | None |
Comments | See MF_00108 and MF_00107 for monofunctional ispD and ispF |