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PDBsum entry 1h5r

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1h5r
Jmol
Contents
Protein chains
290 a.a. *
Ligands
THM ×8
G1P ×4
SO4 ×5
Waters ×473
* Residue conservation analysis
PDB id:
1h5r
Name: Transferase
Title: Thymidylyltransferase complexed with thimidine and glucose-1-phospate
Structure: Glucose-1-phosphate thymidylyltransferase. Chain: a, c, d. Synonym: tdp-glucose synthase, dtdp-glucose pyrophosphorylase. Engineered: yes. Glucose-1-phosphate thymidylyltransferase. Chain: b. Synonym: tdp-glucose synthase, dtdp-glucose pyrophosphorylase.
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
1.9Å     R-factor:   0.173     R-free:   0.234
Authors: C.Rosano,S.Zuccotti,M.Bolognesi
Key ref:
S.Zuccotti et al. (2001). Kinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase. J Mol Biol, 313, 831-843. PubMed id: 11697907 DOI: 10.1006/jmbi.2001.5073
Date:
25-May-01     Release date:   23-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P37744  (RMLA1_ECOLI) -  Glucose-1-phosphate thymidylyltransferase 1
Seq:
Struc:
293 a.a.
290 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.24  - Glucose-1-phosphate thymidylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
6-Deoxyhexose Biosynthesis
      Reaction: dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-alpha-D-glucose
dTTP
Bound ligand (Het Group name = THM)
matches with 58.00% similarity
+
alpha-D-glucose 1-phosphate
Bound ligand (Het Group name = G1P)
corresponds exactly
= diphosphate
+ dTDP-alpha-D-glucose
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     biosynthetic process   5 terms 
  Biochemical function     transferase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.5073 J Mol Biol 313:831-843 (2001)
PubMed id: 11697907  
 
 
Kinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase.
S.Zuccotti, D.Zanardi, C.Rosano, L.Sturla, M.Tonetti, M.Bolognesi.
 
  ABSTRACT  
 
Glucose-1-phosphate thymidylyltransferase is the first enzyme in the biosynthesis of dTDP-l-rhamnose, the precursor of l-rhamnose, an essential component of surface antigens, such as the O-lipopolysaccharide, mediating virulence and adhesion to host tissues in many microorganisms. The enzyme catalyses the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis. To shed more light on the catalytic properties of glucose-1-phosphate thymidylyltransferase from Escherichia coli, specifically distinguishing between ping pong and sequential ordered bi bi reaction mechanisms, the enzyme kinetic properties have been analysed in the presence of different substrates and inhibitors. Moreover, three different complexes of glucose-1-phosphate thymidylyltransferase (co-crystallized with dTDP, with dTMP and glucose-1-phosphate, with d-thymidine and glucose-1-phosphate) have been analysed by X-ray crystallography, in the 1.9-2.3 A resolution range (R-factors of 17.3-17.5 %). The homotetrameric enzyme shows strongly conserved substrate/inhibitor binding modes in a surface cavity next to the topological switch-point of a quasi-Rossmann fold. Inspection of the subunit tertiary structure reveals relationships to other enzymes involved in the biosynthesis of nucleotide-sugars, including distant proteins such as the molybdenum cofactor biosynthesis protein MobA. The precise location of the substrate relative to putative reactive residues in the catalytic center suggests that, in keeping with the results of the kinetic measurements, both catalysed reactions, i.e. dTDP-glucose biosynthesis and pyrophosphorolysis, follow a sequential ordered bi bi catalytic mechanism.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Sequence alignments of G1P-TT and the homologous enzymes glucose-1-phosphate uridylyltransferase (GalF), glucose-1-phosphate adenylyltransferase (GlgC), N-acetylglucosamine-1-phosphate uridylyltransferase (GlmU), and the molybdenum cofactor biosynthesis protein (MobA). The red bracket identifies residues belonging to the PPase consensus sequence segment. Green boxes highlight residues building the G1P-TT active site; red boxes mark residues from the B-site.
Figure 5.
Figure 5. (a) View of the active-site cavity, including the bound dTDP-G molecule (green) and residues that are deemed relevant for recognition and/or electrostatic stabilization of the bound ligand(s) (drawn with DINO.: Visualizing Structural Biology (2001). http://www.bioz.unibas.ch/ not, vert, similar-xray/dino). (b) Stereo view of the B-site residues involved in recognition of the dTDP molecule bound at this site in each G1P-TT subunit.[43 and 44]
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 313, 831-843) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20238176 H.Kim, J.Choi, T.Kim, N.K.Lokanath, S.C.Ha, S.W.Suh, H.Y.Hwang, and K.K.Kim (2010).
Structural basis for the reaction mechanism of UDP-glucose pyrophosphorylase.
  Mol Cells, 29, 397-405.
PDB codes: 3juj 3juk
18807197 D.Simkhada, T.J.Oh, E.M.Kim, J.C.Yoo, and J.K.Sohng (2009).
Cloning and characterization of CalS7 from Micromonospora echinospora sp. calichensis as a glucose-1-phosphate nucleotidyltransferase.
  Biotechnol Lett, 31, 147-153.  
18422615 B.Liu, Y.A.Knirel, L.Feng, A.V.Perepelov, S.N.Senchenkova, Q.Wang, P.R.Reeves, and L.Wang (2008).
Structure and genetics of Shigella O antigens.
  FEMS Microbiol Rev, 32, 627-653.  
18627619 C.J.Zea, G.Camci-Unal, and N.L.Pohl (2008).
Thermodynamics of binding of divalent magnesium and manganese to uridine phosphates: implications for diabetes-related hypomagnesaemia and carbohydrate biocatalysis.
  Chem Cent J, 2, 15.  
18408022 N.Jimenez, R.Canals, M.T.Saló, S.Vilches, S.Merino, and J.M.Tomás (2008).
The Aeromonas hydrophila wb*O34 gene cluster: genetics and temperature regulation.
  J Bacteriol, 190, 4198-4209.  
17434970 D.Aragão, A.M.Fialho, A.R.Marques, E.P.Mitchell, I.Sá-Correia, and C.Frazão (2007).
The complex of Sphingomonas elodea ATCC 31461 glucose-1-phosphate uridylyltransferase with glucose-1-phosphate reveals a novel quaternary structure, unique among nucleoside diphosphate-sugar pyrophosphorylase members.
  J Bacteriol, 189, 4520-4528.
PDB code: 2ux8
18029420 I.Mochalkin, S.Lightle, Y.Zhu, J.F.Ohren, C.Spessard, N.Y.Chirgadze, C.Banotai, M.Melnick, and L.McDowell (2007).
Characterization of substrate binding and catalysis in the potential antibacterial target N-acetylglucosamine-1-phosphate uridyltransferase (GlmU).
  Protein Sci, 16, 2657-2666.
PDB codes: 2v0h 2v0i 2v0j 2v0k 2v0l
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
16085866 E.Silva, A.R.Marques, A.M.Fialho, A.T.Granja, and I.Sá-Correia (2005).
Proteins encoded by Sphingomonas elodea ATCC 31461 rmlA and ugpG genes, involved in gellan gum biosynthesis, exhibit both dTDP- and UDP-glucose pyrophosphorylase activities.
  Appl Environ Microbiol, 71, 4703-4712.  
16206230 J.Bae, K.H.Kim, D.Kim, Y.Choi, J.S.Kim, S.Koh, S.I.Hong, and D.S.Lee (2005).
A practical enzymatic synthesis of UDP sugars and NDP glucoses.
  Chembiochem, 6, 1963-1966.  
15686515 J.M.Cross, M.Clancy, J.R.Shaw, S.K.Boehlein, T.W.Greene, R.R.Schmidt, T.W.Okita, and L.C.Hannah (2005).
A polymorphic motif in the small subunit of ADP-glucose pyrophosphorylase modulates interactions between the small and large subunits.
  Plant J, 41, 501-511.  
15634670 N.M.Koropatkin, W.W.Cleland, and H.M.Holden (2005).
Kinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
  J Biol Chem, 280, 10774-10780.
PDB code: 1wvc
15598657 Z.Zhang, M.Tsujimura, J.Akutsu, M.Sasaki, H.Tajima, and Y.Kawarabayasi (2005).
Identification of an extremely thermostable enzyme with dual sugar-1-phosphate nucleotidylyltransferase activities from an acidothermophilic archaeon, Sulfolobus tokodaii strain 7.
  J Biol Chem, 280, 9698-9705.  
14695508 J.S.Thorson, W.A.Barton, D.Hoffmeister, C.Albermann, and D.B.Nikolov (2004).
Structure-based enzyme engineering and its impact on in vitro glycorandomization.
  Chembiochem, 5, 16-25.  
15292268 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.
PDB code: 1tzf
12837772 A.Matte, J.Sivaraman, I.Ekiel, K.Gehring, Z.Jia, and M.Cygler (2003).
Contribution of structural genomics to understanding the biology of Escherichia coli.
  J Bacteriol, 185, 3994-4002.  
11706035 B.Y.Kwak, Y.M.Zhang, M.Yun, R.J.Heath, C.O.Rock, S.Jackowski, and H.W.Park (2002).
Structure and mechanism of CTP:phosphocholine cytidylyltransferase (LicC) from Streptococcus pneumoniae.
  J Biol Chem, 277, 4343-4350.
PDB codes: 1jyk 1jyl
12171937 J.Sivaraman, V.Sauvé, A.Matte, and M.Cygler (2002).
Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+.
  J Biol Chem, 277, 44214-44219.
PDB code: 1mc3
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 codes are shown on the right.