EzCatDB: S00709
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DB codeS00709
RLCP classification3.133.90030.334 : Transfer
CATH domainDomain 13.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain ACatalytic domain
E.C.2.7.7.33

CATH domainRelated DB codes (homologues)
3.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain AS00465,S00466,D00417,D00859,D00860,T00415

Enzyme Name
UniProtKBKEGG

Q8Z5I4
Protein name
Glucose-1-phosphate cytidylyltransferase
CDP glucose pyrophosphorylase
Cytidine diphosphoglucose pyrophosphorylase
Cytidine diphosphate glucose pyrophosphorylase
Cytidine diphosphate-D-glucose pyrophosphorylase
CTP:D-glucose-1-phosphate cytidylyltransferase
SynonymsGlucose-1-phosphate cytidylyltransferase
EC 2.7.7.33
RefSeqNP_804622.1 (Protein)
NC_004631.1 (DNA/RNA sequence)
PfamPF00483 (NTP_transferase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00500Starch and sucrose metabolism
MAP00520Nucleotide sugars metabolism

UniProtKB:Accession NumberQ8Z5I4
Entry nameRFBF_SALTI
ActivityCTP + alpha-D-glucose 1-phosphate = diphosphate + CDP-glucose.
SubunitHomoexamer.
Subcellular location
CofactorBinds 1 magnesium ion per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00063C00103C00013C00501
CompoundMagnesiumCTPalpha-D-glucose 1-phosphatediphosphateCDP-glucose
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidecarbohydrate,phosphate group/phosphate ionphosphate group/phosphate ionamide group,amine group,carbohydrate,nucleotide
ChEBI18420
17677
29042
29888
28942
PubChem888
6176
65533
21961011
1023
439244
             
1tzfA00Bound:_MGUnboundUnboundUnboundBound:C5G
1wvcA00Bound:2x_MGBound:CTPUnboundUnboundUnbound

Active-site residues
resource
literature [3], [5], [7]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1tzfA00      ;LYS 25;ARG 111;LYS 179
ASP 131;ASP 236(Magnesium binding)
LEU 12;GLY 13;      
invisible 12-21
1wvcA00ARG 15;LYS 25;ARG 111;       
ASP 131;ASP 236(Magnesium binding)
LEU 12;GLY 13;THR 14
invisible 163, 178-179

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Fig.1A, p.6657-6658
[5]p.548-549
[6]Fig. 3B, p.44027
[7]Fig. 4, p10778-10780

references
[1]
PubMed ID8276783
JournalJ Biol Chem
Year1994
Volume269
Pages122-6
AuthorsLindqvist L, Kaiser R, Reeves PR, Lindberg AA
TitlePurification, characterization, and high performance liquid chromatography assay of Salmonella glucose-1-phosphate cytidylyltransferase from the cloned rfbF gene.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF THE TRUNCATED FORM AND IN COMPLEX WITH UDP-GLCNAC
PubMed ID10428949
JournalEMBO J
Year1999
Volume18
Pages4096-107
AuthorsBrown K, Pompeo F, Dixon S, Mengin-Lecreulx D, Cambillau C, Bourne Y
TitleCrystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily.
Related PDB1fwy,1fxj
Related UniProtKBP0ACC7
[3]
CommentsX-RAY CRYSTALLOGRAPHY
PubMed ID11118200
JournalEMBO J
Year2000
Volume19
Pages6652-63
AuthorsBlankenfeldt W, Asuncion M, Lam JS, Naismith JH
TitleThe structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
Related PDB1fxo,1fzw,1g0r,1g1l,1g23,1g2v,1g3l
[4]
CommentsCHARACTERIZATION, X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEXES WITH DTDP-G; DTMP AND G1P AND DEOXYTHYMIDINE AND G1P
PubMed ID11697907
JournalJ Mol Biol
Year2001
Volume313
Pages831-43
AuthorsZuccotti S, Zanardi D, Rosano C, Sturla L, Tonetti M, Bolognesi M
TitleKinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase.
Related PDB1h5r,1h5s,1h5t
Related UniProtKBP37744
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-291
PubMed ID11373625
JournalNat Struct Biol
Year2001
Volume8
Pages545-51
AuthorsBarton WA, Lesniak J, Biggins JB, Jeffrey PD, Jiang J, Rajashankar KR, Thorson JS, Nikolov DB
TitleStructure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization.
Related PDB1iim,1iin
Related UniProtKBQ9F7K6
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
PubMed ID15292268
JournalJ Biol Chem
Year2004
Volume279
Pages44023-9
AuthorsKoropatkin NM, Holden HM
TitleMolecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
Related PDB1tzf
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
PubMed ID15634670
JournalJ Biol Chem
Year2005
Volume280
Pages10774-80
AuthorsKoropatkin NM, Cleland WW, Holden HM
TitleKinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
Related PDB1wvc
[8]
PubMed ID16895327
JournalChem Rev
Year2006
Volume106
Pages3252-78
AuthorsCleland WW, Hengge AC
TitleEnzymatic mechanisms of phosphate and sulfate transfer.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
PubMed ID17567737
JournalProtein Sci
Year2007
Volume16
Pages1379-88
AuthorsThoden JB, Holden HM
TitleActive site geometry of glucose-1-phosphate uridylyltransferase.
Related PDB2pa4

comments
This enzyme, Glucose-1-phosphate cytidylyltransferase (EC 2.7.7.33), is homologous to Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24; S00465 in EzCatDB).
According to the literature [6[ and [7], the reaction proceeds as follows:
(0) Sidechain of Arg15, along with mainchain amide groups of resideus Leu12, Gly13 and Thr14, and a magnesium bound to gamma-phosphate group, stabilize the negative charge on the leaving group, beta- and gamma-phosphate groups of CTP, whereas Lys25 and another magnesium ion which is bound to Asp131 and Asp236 may stabilize the negative charge on alpha-phosphate group of CTP. Meanwhile, Lys179 from adjacent subunit may stabilize the phosphate group of Glucose 1-phosphate.
(1) The phosphoryl oxygen of Glucose 1-phosphate makes a nucleophilic attack on the alpha-phosphate group of CTP, leading to the transition-state (SN2-like reaction).
(2) The transition-state must be stabilized by sidechains of Arg15, Lys25 and Lys179, mainchain amide groups of residues 12 to 14, and the two magnesium ions bound to phosphate groups of CTP.
(3) Finally, diphosphate is released from CTP, forming CDP-glucose.

createdupdated
2009-03-312011-12-02


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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