DB code: S00709

RLCP classification 3.133.90030.334 : Transfer
CATH domain 3.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A Catalytic domain
E.C. 2.7.7.33
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A S00465 S00466 D00417 D00859 D00860 T00415

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q8Z5I4
Glucose-1-phosphate cytidylyltransferase
EC 2.7.7.33
NP_804622.1 (Protein)
NC_004631.1 (DNA/RNA sequence)
PF00483 (NTP_transferase)
[Graphical View]

KEGG enzyme 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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q8Z5I4 RFBF_SALTI CTP + alpha-D-glucose 1-phosphate = diphosphate + CDP-glucose. Homoexamer. Binds 1 magnesium ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00500 Starch and sucrose metabolism
MAP00520 Nucleotide sugars metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00063 C00103 C00013 C00501
E.C.
Compound Magnesium CTP alpha-D-glucose 1-phosphate diphosphate CDP-glucose
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide carbohydrate,phosphate group/phosphate ion phosphate group/phosphate ion amide group,amine group,carbohydrate,nucleotide
ChEBI 18420
17677
29042
29888
28942
PubChem 888
6176
65533
1023
21961011
439244
1tzfA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Bound:C5G
1wvcA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Bound:CTP Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [3], [5], [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1tzfA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;LYS 25;ARG 111;LYS 179 ASP 131;ASP 236(Magnesium binding) LEU 12;GLY 13; invisible 12-21
1wvcA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 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
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 8276783
Journal J Biol Chem
Year 1994
Volume 269
Pages 122-6
Authors Lindqvist L, Kaiser R, Reeves PR, Lindberg AA
Title Purification, characterization, and high performance liquid chromatography assay of Salmonella glucose-1-phosphate cytidylyltransferase from the cloned rfbF gene.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF THE TRUNCATED FORM AND IN COMPLEX WITH UDP-GLCNAC
Medline ID
PubMed ID 10428949
Journal EMBO J
Year 1999
Volume 18
Pages 4096-107
Authors Brown K, Pompeo F, Dixon S, Mengin-Lecreulx D, Cambillau C, Bourne Y
Title Crystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily.
Related PDB 1fwy 1fxj
Related UniProtKB P0ACC7
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID
PubMed ID 11118200
Journal EMBO J
Year 2000
Volume 19
Pages 6652-63
Authors Blankenfeldt W, Asuncion M, Lam JS, Naismith JH
Title The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
Related PDB 1fxo 1fzw 1g0r 1g1l 1g23 1g2v 1g3l
Related UniProtKB
[4]
Resource
Comments CHARACTERIZATION, X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEXES WITH DTDP-G; DTMP AND G1P AND DEOXYTHYMIDINE AND G1P
Medline ID
PubMed ID 11697907
Journal J Mol Biol
Year 2001
Volume 313
Pages 831-43
Authors Zuccotti S, Zanardi D, Rosano C, Sturla L, Tonetti M, Bolognesi M
Title Kinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase.
Related PDB 1h5r 1h5s 1h5t
Related UniProtKB P37744
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-291
Medline ID
PubMed ID 11373625
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 545-51
Authors Barton WA, Lesniak J, Biggins JB, Jeffrey PD, Jiang J, Rajashankar KR, Thorson JS, Nikolov DB
Title Structure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization.
Related PDB 1iim 1iin
Related UniProtKB Q9F7K6
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
Medline ID
PubMed ID 15292268
Journal J Biol Chem
Year 2004
Volume 279
Pages 44023-9
Authors Koropatkin NM, Holden HM
Title Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
Related PDB 1tzf
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID
PubMed ID 15634670
Journal J Biol Chem
Year 2005
Volume 280
Pages 10774-80
Authors Koropatkin NM, Cleland WW, Holden HM
Title Kinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
Related PDB 1wvc
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 16895327
Journal Chem Rev
Year 2006
Volume 106
Pages 3252-78
Authors Cleland WW, Hengge AC
Title Enzymatic mechanisms of phosphate and sulfate transfer.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
Medline ID
PubMed ID 17567737
Journal Protein Sci
Year 2007
Volume 16
Pages 1379-88
Authors Thoden JB, Holden HM
Title Active site geometry of glucose-1-phosphate uridylyltransferase.
Related PDB 2pa4
Related UniProtKB

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.

Created Updated
2009-03-31 2011-12-02