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PDBsum entry 1tzf

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protein ligands metals links
Transferase PDB id
1tzf
Jmol
Contents
Protein chain
251 a.a. *
Ligands
C5G
Metals
_MG
Waters ×162
* Residue conservation analysis
PDB id:
1tzf
Name: Transferase
Title: X-ray crystal structure of alpha-d-glucose-1-phosphate cytidylyltransferase from salmonella typhi
Structure: Glucose-1-phosphate cytidylyltransferase. Chain: a. Synonym: alpha-d-glucose-1-phosphate cytidylyltransferase. Glucose pyrophosphorylase. Engineered: yes. Other_details: complexed with cytidyl-5'-phosphate-glucosyl phosphate
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:
2.10Å     R-factor:   0.199     R-free:   0.248
Authors: N.M.Koropatkin,H.M.Holden
Key ref:
N.M.Koropatkin and H.M.Holden (2004). Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi. J Biol Chem, 279, 44023-44029. PubMed id: 15292268 DOI: 10.1074/jbc.M407755200
Date:
09-Jul-04     Release date:   07-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26396  (RFBF_SALTY) -  Glucose-1-phosphate cytidylyltransferase
Seq:
Struc:
257 a.a.
251 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
+ alpha-D-glucose 1-phosphate
= diphosphate
+
CDP-glucose
Bound ligand (Het Group name = C5G)
corresponds exactly
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.M407755200 J Biol Chem 279:44023-44029 (2004)
PubMed id: 15292268  
 
 
Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
N.M.Koropatkin, H.M.Holden.
 
  ABSTRACT  
 
Dideoxysugars, which display biological activities ranging from mediating cell-cell interactions to serving as components in some antibiotics, are synthesized in various organisms via complex biochemical pathways that begin with the attachment of alpha-D-glucose 1-phosphate to either CTP or dTTP. Here we describe the three-dimensional structure of the alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi, which catalyzes the first step in the production of CDP-tyvelose. For this investigation, the enzyme was crystallized in the presence of its product, CDP-glucose. In contrast to previous reports, the enzyme exists as a fully integrated hexamer with 32-point group symmetry. Each subunit displays a "bird-like" appearance with the "body" composed predominantly of a seven-stranded mixed beta-sheet and the two "wings" formed by beta-hairpin motifs. These two wings mediate subunit-subunit interactions along the 3-fold and 2-fold rotational axes, respectively. The six active sites of the hexamer are situated between the subunits related by the 2-fold rotational axes. CDP-glucose is anchored to the protein primarily by hydrogen bonds with backbone carbonyl oxygens and peptidic NH groups. The side chains of Arg111 and Asn188 from one subunit and Glu178 and Lys179 from the second subunit are also involved in hydrogen bonding with the ligand. The topology of the main core domain bears striking similarity to that observed for glucose-1-phosphate thymidylyltransferase and 4-diphosphocytidyl-2-C-methylerythritol synthetase.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Electron density corresponding to the CDP-glucose moiety. The map shown 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 the coordinates for the ligand. The map was contoured at 4 .
Figure 3.
FIG. 3. The active site of glucose-1-phosphate cytidylyltransferase. Shown in a is the location of the bound CDP-glucose ligand in context with the tertiary structure of the protein. The color coding for the ribbon representation is as described in Fig. 2. Note that the ribbon representation depicted in magenta corresponds to the second subunit forming the active site. Those amino acid residues located within 3.6 Å of the CDP-glucose are displayed in b. For clarity, Gly11 was omitted from the figure. Residues corresponding to the second subunit forming the active site are displayed in magenta.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 44023-44029) copyright 2004.  
  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
15805590 N.M.Koropatkin, and H.M.Holden (2005).
Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose.
  Acta Crystallogr D Biol Crystallogr, 61, 365-373.
PDB code: 1wvg
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.