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HAMAP rule MF_01520

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General rule information [?]

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 [?]


Identifier, protein and gene names [?]

Identifier
ISPDF
Protein name
RecName: Full=Bifunctional enzyme IspD/IspF;
Includes:
RecName: Full=2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase;
EC 2.7.7.60;
AltName: Full=4-diphosphocytidyl-2C-methyl-D-erythritol synthase;
AltName: Full=MEP cytidylyltransferase;
Short=MCT;
Includes:
RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase;
Short=MECPP-synthase;
Short=MECDP-synthase;
Short=MECPS;
EC 4.6.1.12;
Gene name
ispDF

Comments [?]

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
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 [?]

Isoprene biosynthesis
Lyase
Metal-binding
Multifunctional enzyme
Nucleotidyltransferase
Transferase

Gene Ontology [?]

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.

Cross-references [?]

Pfam PF01128; IspD; 1;
PF02542; YgbB; 1;
NCBIfam TIGR00453; IspD; 1;
TIGR00151; IspF; 1;
PROSITE PS01295; ISPD; 1;
PS01350; ISPF; 1;

Features [?]

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 [?]

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


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