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PDBsum entry 1wvc

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protein ligands metals links
Transferase PDB id
1wvc
Jmol
Contents
Protein chain
254 a.a. *
Ligands
CTP
Metals
_MG ×2
_NI
Waters ×91
* Residue conservation analysis
PDB id:
1wvc
Name: Transferase
Title: Alpha-d-glucose-1-phosphate cytidylyltransferase complexed w
Structure: Glucose-1-phosphate cytidylyltransferase. Chain: a. Synonym: alpha-d-glucose-1-phosphate cytidylyltransferase, glucose pyrophosphorylase. Engineered: yes
Source: Salmonella enterica subsp. Enterica se typhi. Organism_taxid: 220341. Strain: ct18. Gene: rfbf. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.50Å     R-factor:   0.202     R-free:   0.272
Authors: N.M.Koropatkin,W.W.Cleland,H.M.Holden
Key ref:
N.M.Koropatkin et al. (2005). Kinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi. J Biol Chem, 280, 10774-10780. PubMed id: 15634670 DOI: 10.1074/jbc.M414111200
Date:
14-Dec-04     Release date:   11-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8Z5I4  (RFBF_SALTI) -  Glucose-1-phosphate cytidylyltransferase
Seq:
Struc:
257 a.a.
254 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.33  - Glucose-1-phosphate cytidylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
CDP-abequose, CDP-ascarylose, CDP-pararose and CDP-tyrelose Biosynthesis
      Reaction: CTP + alpha-D-glucose 1-phosphate = diphosphate + CDP-glucose
CTP
Bound ligand (Het Group name = CTP)
corresponds exactly
+ alpha-D-glucose 1-phosphate
= diphosphate
+ CDP-glucose
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   3 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M414111200 J Biol Chem 280:10774-10780 (2005)
PubMed id: 15634670  
 
 
Kinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
N.M.Koropatkin, W.W.Cleland, H.M.Holden.
 
  ABSTRACT  
 
Tyvelose is a 3,6-dideoxyhexose found in the O-antigen of the surface lipopolysaccharides of some pathogenic bacteria. It is synthesized via a complex biochemical pathway that is initiated by the formation of CDP-D-glucose. The production of this ligand is catalyzed by the enzyme glucose-1-phosphate cytidylyltransferase, which utilizes alpha-D-glucose 1-phosphate and MgCTP as substrates. Previous x-ray crystallographic investigations have demonstrated that the Salmonella typhi enzyme complexed with the product CDP-glucose is a fully integrated hexamer displaying 32 point group symmetry. The binding pocket for CDP-glucose is shared between two subunits. Here we describe both a detailed kinetic analysis of the cytidylyltransferase and a structural investigation of the enzyme complexed with MgCTP. These data demonstrate that the reaction catalyzed by the cytidylyltransferase proceeds via a sequential rather than a Bi Bi ping-pong mechanism as was previously reported. Additionally, the enzyme utilizes both CTP and UTP equally well as substrates. The structure of the enzyme with bound MgCTP reveals that the binding pocket for the nucleotide is contained within one subunit rather than shared between two. Key side chains involved in nucleotide binding include Thr(14), Arg(15), Lys(25), and Arg(111). In the previous structure of the enzyme complexed with CDP-glucose, those residues defined by Thr(14) to Ile(21) were disordered. The kinetic and x-ray crystallographic data presented here support a mechanism for this enzyme that is similar to that reported for the glucose-1-phosphate thymidylyltransferases.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Ribbon representation of glucose-1-phosphate cytidylyltransferase from S. typhi. The cytidylyltransferase from S. typhi is a hexamer displaying 32 symmetry. For the sake of clarity, only half of the hexamer is shown. The active sites are indicated by the positions of the CDP-glucose ligands, which are displayed in ball-and-stick representations.
Figure 3.
FIG. 3. Representative electron density. Shown is the electron density corresponding to the nucleotide. The map was calculated with coefficients of the form (F[o] - F[c]), where F[o] was the native structure factor amplitude and F[c] was the calculated structure factor amplitude from the model lacking coordinates for the MgCTP ligand. The map was contoured at 3 . There were two magnesium ions modeled into the electron density and they are represented by the green spheres.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 10774-10780) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19330326 X.Q.Qi, Q.L.Sun, L.P.Bai, J.J.Shan, Y.Zhang, R.Zhang, and Y.Li (2009).
Identification of alpha-D-glucose-1-phosphate cytidylyltransferase involved in Ebosin biosynthesis of Streptomyces sp. 139.
  Appl Microbiol Biotechnol, 83, 361-368.  
17322528 J.B.Thoden, and H.M.Holden (2007).
The molecular architecture of glucose-1-phosphate uridylyltransferase.
  Protein Sci, 16, 432-440.
PDB code: 2e3d
17567737 J.B.Thoden, and H.M.Holden (2007).
Active site geometry of glucose-1-phosphate uridylyltransferase.
  Protein Sci, 16, 1379-1388.
PDB code: 2pa4
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