Glycerol-3-phosphate cytidylyltransferase

 

Glycerol-3-phosphate cytidylyltransferase catalyses the transfer of the cytidylyl group of CTP to sn-glycerol 3-phosphate so the activated glycerol 3-phosphate can be used for the biosynthesis of teichoic acid linkage units in bacterial cell walls.

 

Reference Protein and Structure

Sequence
P27623 UniProt (2.7.7.39) IPR006409 (Sequence Homologues) (PDB Homologues)
Biological species
Bacillus subtilis subsp. subtilis str. 168 (Bacteria) Uniprot
PDB
1n1d - Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol (2.0 Å) PDBe PDBsum 1n1d
Catalytic CATH Domains
3.40.50.620 CATHdb (see all for 1n1d)
Cofactors
Magnesium(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:2.7.7.39)

hydron
CHEBI:15378ChEBI
+
CTP(4-)
CHEBI:37563ChEBI
+
sn-glycerol 3-phosphate(2-)
CHEBI:57597ChEBI
→
diphosphate(3-)
CHEBI:33019ChEBI
+
(2R)-CDP-glycerol(2-)
CHEBI:58311ChEBI
Alternative enzyme names: CDP-glycerol pyrophosphorylase, CTP:glycerol 3-phosphate cytidylyltransferase, Gro-PCT, Cytidine diphosphate glycerol pyrophosphorylase, Cytidine diphosphoglycerol pyrophosphorylase, CDP-glycerol diphosphorylase, TagD (gene name), TarD (gene name),

Enzyme Mechanism

Introduction

Proceeds via a random order reaction mechanism where there is negative cooperativity in the binding of substrates but not in catalysis. Several residues has been implicated in regulating a negative cooperativity between the binding of glycerol-3-phosphate and CTP. However, the NMR and crystallographic data characterising such residues are inconsistent, and as of yet have not explicitly identified the role that individual residues play.

Catalytic Residues Roles

UniProt PDB* (1n1d)
Lys44, Lys46 Lys44A, Lys46A Help stabilise the negatively charged transition state. attractive charge-charge interaction, hydrogen bond donor, electrostatic stabiliser
*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

bimolecular nucleophilic substitution, overall reactant used, overall product formed, native state of enzyme regenerated, rate-determining step

References

  1. Pattridge KA et al. (2003), J Biol Chem, 278, 51863-51871. Glycerol-3-phosphate Cytidylyltransferase: STRUCTURAL CHANGES INDUCED BY BINDING OF CDP-GLYCEROL AND THE ROLE OF LYSINE RESIDUES IN CATALYSIS. DOI:10.1074/jbc.m306174200. PMID:14506262.
  2. Mericl AN et al. (2012), Med Sci Monit, 18, BR427-BR434. Comparative kinetic analysis of glycerol 3-phosphate cytidylyltransferase from Enterococcus faecalis and Listeria monocytogenes. DOI:10.12659/MSM.883535.
  3. Weber CH et al. (1999), Structure, 7, 1113-1124. A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from Bacillus subtilis. DOI:10.1016/s0969-2126(99)80178-6. PMID:10508782.
  4. Carter CW Jr (1993), Annu Rev Biochem, 62, 715-748. Cognition, Mechanism, and Evolutionary Relationships in Aminoacyl-tRNA Synthetases. DOI:10.1146/annurev.bi.62.070193.003435. PMID:8352600.

Step 1. The glycerol-3-phosphate initiates a nucleophilic attack on the alpha phosphate of CTP in a substitution reaction. . The magnesium enhances the electrophilicity of the CTP alpha phosphate by reducing the repulsion between this group and the attacking nucleophile. Kinetic studies have shown the divalent magnesium ion to be essential for catalysis. Pattridge et al. [PMID:14506262] suggests that the ion coordinates between the alpha phosphate of the CTP and the attacking phosphate of glycerol-3-phosphate [PMID:14506262].

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Catalytic Residues Roles

Residue Roles
Lys46A attractive charge-charge interaction, hydrogen bond donor, electrostatic stabiliser
Lys44A attractive charge-charge interaction, hydrogen bond donor, electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic substitution, overall reactant used, overall product formed, native state of enzyme regenerated, rate-determining step
Download: Image, Marvin File

Step 1. The glycerol-3-phosphate initiates a nucleophilic attack on the alpha phosphate of CTP in a substitution reaction. . The magnesium enhances the electrophilicity of the CTP alpha phosphate by reducing the repulsion between this group and the attacking nucleophile. Kinetic studies have shown the divalent magnesium ion to be essential for catalysis. Pattridge et al. [PMID:14506262] suggests that the ion coordinates between the alpha phosphate of the CTP and the attacking phosphate of glycerol-3-phosphate [PMID:14506262].

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday, Charity Hornby