M-CSA Mechanism and Catalytic Site Atlas

4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase

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.

Reference Protein and Structure

Sequence: Q8FI04 (2.7.1.148) (Sequence Homologues) (PDB Homologues)
Biological species: Escherichia coli CFT073 (Bacteria)
PDB: 1oj4 - Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (2.01 Å)
Catalytic CATH Domains: 3.30.230.10 (see all for 1oj4)
Cofactors: Magnesium(2+) (1)

Click To Show Structure

Enzyme Reaction (EC:2.7.1.148)

4-CDP-2-C-methyl-D-erythritol(2-)

CHEBI:57823

ATP(4-)

CHEBI:30616

→

ADP(3-)

CHEBI:456216

4-CDP-2-C-methyl-D-erythritol 2-phosphate(4-)

CHEBI:57919

hydron

CHEBI:15378

Enzyme reaction links: IntEnz ENZYME ExplorEnz

Alternative enzyme names: CDP-ME kinase, CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase,

Enzyme Mechanism

Mechanism Proposal 1 ☆☆☆

Summary
Step 1
Step 2
Products
All Steps

Introduction

The catalysis is most likely to follow an associative in-line mechanism to form a pentacovalent intermediate. Asp141 acts as a base to deprotonate the hydroxyl group of CDP-ME to promote its nucleophilic attack on the terminal phosphate of ATP. Lys10 stabilises the transition state by interacting with the oxygen of the hydroxyl group. Additionally, a magnesium cation is needed for catalysis but no crystal structure of CDP-ME has been solved with the cofactor present.

Catalytic Residues Roles

UniProt	PDB* (1oj4)
Lys10	Lys10A	It stabilises the transition state by interacting with the oxygen atom of the substrate hydroxyl group.	hydrogen bond donor, electrostatic stabiliser
Asp141	Asp141A	It acts as a base to deprotonate the hydroxyl group of CDP-ME to promote its nucleophilic attack on the terminal phosphate of ATP.	activator, proton acceptor, proton donor

*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic substitution, overall product formed, overall reactant used, native state of enzyme regenerated

References

Miallau L et al. (2003), Proc Natl Acad Sci U S A, 100, 9173-9178. Biosynthesis of isoprenoids: Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol kinase. DOI:10.1073/pnas.1533425100. PMID:12878729.
Frank A et al. (2017), Chem Rev, 117, 5675-5703. The Methylerythritol Phosphate Pathway to Isoprenoids. DOI:10.1021/acs.chemrev.6b00537. PMID:27995802.
Wada T et al. (2003), J Biol Chem, 278, 30022-30027. Crystal Structure of 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase, an Enzyme in the Non-mevalonate Pathway of Isoprenoid Synthesis. DOI:10.1074/jbc.m304339200. PMID:12771135.

Step 1. Asp141 deprotonates the hydroxyl group on the substrate. This increases the nucleophilicity of the substract to then attack the gamma phosphate on ATP in an inline nucleophilic substitution.

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