EzCatDB: S00318
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DB codeS00318
RLCP classification3.133.90010.373 : Transfer
CATH domainDomain 13.40.50.620 : Rossmann foldCatalytic domain
E.C.2.7.7.39
MACiEM0296

CATH domainRelated DB codes (homologues)
3.40.50.620 : Rossmann foldS00314,S00549,S00316,S00317,S00315,T00085,T00249,D00300,M00177,M00178,T00106,T00114

Enzyme Name
UniProtKBKEGG

P27623
Protein nameGlycerol-3-phosphate cytidylyltransferaseglycerol-3-phosphate cytidylyltransferase
CDP-glycerol pyrophosphorylase
cytidine diphosphoglycerol pyrophosphorylase
cytidine diphosphate glycerol pyrophosphorylase
CTP:glycerol 3-phosphate cytidylyltransferase
Gro-PCT
SynonymsGCT
Gro-PCT
EC 2.7.7.39
CDP-glycerol pyrophosphorylase
Teichoic acid biosynthesis protein D
RefSeqNP_391455.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PfamPF01467 (CTP_transf_2)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00564Glycerophospholipid metabolism

UniProtKB:Accession NumberP27623
Entry nameTAGD_BACSU
ActivityCTP + sn-glycerol 3-phosphate = diphosphate + CDP-glycerol.
SubunitHomodimer.
Subcellular locationCytoplasm.
CofactorDivalent metal cations. Prefers cobalt, magnesium, manganese or iron.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00063C00093C00013C00513
CompoundMagnesiumCTPsn-Glycerol 3-phosphatePyrophosphateCDPglycerol
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidecarbohydrate,phosphate group/phosphate ionphosphate group/phosphate ionamine group,carbohydrate,nucleotide
ChEBI18420
17677
15978
29888
17885
PubChem888
6176
439162
21961011
1023
439249
             
1cozAUnboundBound:CTPUnboundUnboundUnbound
1cozBUnboundBound:CTPUnboundUnboundUnbound
1n1dAUnboundUnboundUnboundAnalogue:SO4Bound:C2G
1n1dBUnboundUnboundUnboundAnalogue:SO4Bound:C2G
1n1dCUnboundUnboundUnboundUnboundBound:C2G
1n1dDUnboundUnboundUnboundAnalogue:SO4Bound:C2G

Active-site residues
resource
literature [2],[3] & [7]
pdbCatalytic residuesCofactor-binding residues
          
1cozAHIS  14;HIS  17;LYS  44;LYS  46
ASP  94(Magnesium binding)
1cozBHIS 514;HIS 517;LYS 544;LYS 546
ASP 594(Magnesium binding)
1n1dAHIS  14;HIS  17;LYS  44;LYS  46
ASP  94(Magnesium binding)
1n1dBHIS  14;HIS  17;LYS  44;LYS  46
ASP  94(Magnesium binding)
1n1dCHIS  14;HIS  17;LYS  44;LYS  46
ASP  94(Magnesium binding)
1n1dDHIS  14;HIS  17;LYS  44;LYS  46
ASP  94(Magnesium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.5, p.15165-151662
[3]Fig.4, p.1117-1121
[7]p.51866-51870

references
[1]
PubMed ID7479698
JournalProteins
Year1995
Volume22
Pages259-66
AuthorsBork P, Holm L, Koonin EV, Sander C
TitleThe cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction.
[2]
PubMed ID9182537
JournalJ Biol Chem
Year1997
Volume272
Pages15161-6
AuthorsPark YS, Gee P, Sanker S, Schurter EJ, Zuiderweg ER, Kent C
TitleIdentification of functional conserved residues of CTP:glycerol-3-phosphate cytidylyltransferase. Role of histidines in the conserved HXGH in catalysis.
[3]
PubMed ID10508782
JournalStructure Fold Des
Year1999
Volume7
Pages1113-24
AuthorsWeber CH, Park YS, Sanker S, Kent C, Ludwig ML
TitleA prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
Related PDB1coz
Related UniProtKBP27623
[4]
PubMed ID11487587
JournalJ Biol Chem
Year2001
Volume276
Pages37922-8
AuthorsSanker S, Campbell HA, Kent C
TitleNegative cooperativity of substrate binding but not enzyme activity in wild-type and mutant forms of CTP:glycerol-3-phosphate cytidylyltransferase.
[5]
PubMed ID11685240
JournalNat Struct Biol
Year2001
Volume8
Pages947-52
AuthorsStevens SY, Sanker S, Kent C, Zuiderweg ER
TitleDelineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity.
[6]
PubMed ID12637027
JournalBiochim Biophys Acta
Year2003
Volume1646
Pages196-206
AuthorsBadurina DS, Zolli-Juran M, Brown ED
TitleCTP:glycerol 3-phosphate cytidylyltransferase (TarD) from Staphylococcus aureus catalyzes the cytidylyl transfer via an ordered Bi-Bi reaction mechanism with micromolar K(m) values.
[7]
PubMed ID14506262
JournalJ Biol Chem
Year2003
Volume278
Pages51863-71
AuthorsPattridge KA, Weber CH, Friesen JA, Sanker S, Kent C, Ludwig ML
TitleGlycerol-3-phosphate cytidylyltransferase. Structural changes induced by binding of CDP-glycerol and the role of lysine residues in catalysis.
Related PDB1n1d

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.

createdupdated
2002-05-292009-02-26


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