DB code: S00318

RLCP classification 3.133.90010.373 : Transfer
CATH domain 3.40.50.620 : Rossmann fold Catalytic domain
E.C. 2.7.7.39
CSA
M-CSA
MACiE M0296

CATH domain Related DB codes (homologues)
3.40.50.620 : Rossmann fold S00314 S00549 S00316 S00317 S00315 T00085 T00249 D00300 M00177 M00178 T00106 T00114

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P27623 Glycerol-3-phosphate cytidylyltransferase
GCT
Gro-PCT
EC 2.7.7.39
CDP-glycerol pyrophosphorylase
Teichoic acid biosynthesis protein D
NP_391455.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PF01467 (CTP_transf_2)
[Graphical View]

KEGG enzyme name
glycerol-3-phosphate cytidylyltransferase
CDP-glycerol pyrophosphorylase
cytidine diphosphoglycerol pyrophosphorylase
cytidine diphosphate glycerol pyrophosphorylase
CTP:glycerol 3-phosphate cytidylyltransferase
Gro-PCT

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P27623 TAGD_BACSU CTP + sn-glycerol 3-phosphate = diphosphate + CDP-glycerol. Homodimer. Cytoplasm. Divalent metal cations. Prefers cobalt, magnesium, manganese or iron.

KEGG Pathways
Map code Pathways E.C.
MAP00564 Glycerophospholipid metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00063 C00093 C00013 C00513
E.C.
Compound Magnesium CTP sn-Glycerol 3-phosphate Pyrophosphate CDPglycerol
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide carbohydrate,phosphate group/phosphate ion phosphate group/phosphate ion amine group,carbohydrate,nucleotide
ChEBI 18420
17677
15978
29888
17885
PubChem 888
6176
439162
1023
21961011
439249
1cozA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:CTP Unbound Unbound Unbound
1cozB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:CTP Unbound Unbound Unbound
1n1dA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4 Bound:C2G
1n1dB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4 Bound:C2G
1n1dC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:C2G
1n1dD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4 Bound:C2G

Reference for Active-site residues
resource references E.C.
literature [2],[3] & [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1cozA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 14;HIS 17;LYS 44;LYS 46 ASP 94(Magnesium binding)
1cozB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 514;HIS 517;LYS 544;LYS 546 ASP 594(Magnesium binding)
1n1dA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 14;HIS 17;LYS 44;LYS 46 ASP 94(Magnesium binding)
1n1dB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 14;HIS 17;LYS 44;LYS 46 ASP 94(Magnesium binding)
1n1dC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 14;HIS 17;LYS 44;LYS 46 ASP 94(Magnesium binding)
1n1dD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 14;HIS 17;LYS 44;LYS 46 ASP 94(Magnesium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.5, p.15165-15166 2
[3]
Fig.4, p.1117-1121
[7]
p.51866-51870

References
[1]
Resource
Comments
Medline ID
PubMed ID 7479698
Journal Proteins
Year 1995
Volume 22
Pages 259-66
Authors Bork P, Holm L, Koonin EV, Sander C
Title The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9182537
Journal J Biol Chem
Year 1997
Volume 272
Pages 15161-6
Authors Park YS, Gee P, Sanker S, Schurter EJ, Zuiderweg ER, Kent C
Title Identification of functional conserved residues of CTP:glycerol-3-phosphate cytidylyltransferase. Role of histidines in the conserved HXGH in catalysis.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 10508782
Journal Structure Fold Des
Year 1999
Volume 7
Pages 1113-24
Authors Weber CH, Park YS, Sanker S, Kent C, Ludwig ML
Title A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
Related PDB 1coz
Related UniProtKB P27623
[4]
Resource
Comments
Medline ID
PubMed ID 11487587
Journal J Biol Chem
Year 2001
Volume 276
Pages 37922-8
Authors Sanker S, Campbell HA, Kent C
Title Negative cooperativity of substrate binding but not enzyme activity in wild-type and mutant forms of CTP:glycerol-3-phosphate cytidylyltransferase.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 11685240
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 947-52
Authors Stevens SY, Sanker S, Kent C, Zuiderweg ER
Title Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 12637027
Journal Biochim Biophys Acta
Year 2003
Volume 1646
Pages 196-206
Authors Badurina DS, Zolli-Juran M, Brown ED
Title CTP:glycerol 3-phosphate cytidylyltransferase (TarD) from Staphylococcus aureus catalyzes the cytidylyl transfer via an ordered Bi-Bi reaction mechanism with micromolar K(m) values.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 14506262
Journal J Biol Chem
Year 2003
Volume 278
Pages 51863-71
Authors Pattridge KA, Weber CH, Friesen JA, Sanker S, Kent C, Ludwig ML
Title Glycerol-3-phosphate cytidylyltransferase. Structural changes induced by binding of CDP-glycerol and the role of lysine residues in catalysis.
Related PDB 1n1d
Related UniProtKB

Comments
The paper [2] suggested that negatively charged oxygen of phoshate group from substrate, grycerol-3-phosphate, makes a nucleophilic attack at the alpha-phosphorous atom of another substrate, CTP, forming a pentacoordinate transition state.
The literature, [2], [3] and [7], reported that positively charged residues, His14, His17, Lys44 and Lys46, stabilize the transition state. Moreover, magnesium ion is essential for this catalysis, although its binding site has not been determined (see [7]). This divalent ion is presumed to bridge the phosphate groups of substrates and products, possibly stablizing the negative charge on the two phosphate groupsm (see [7]). In the structure of 1n1d (PDB), water (HOH 745) may replace the position of magnesium ion, which should be bound to Asp94 (see [7]). Taken together, the metal ion possibly interacts with the transferred and acceptor phosphate groups.

Created Updated
2002-05-29 2009-02-26