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PDBsum entry 1mc3

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1mc3
Jmol
Contents
Protein chains
291 a.a. *
Ligands
TTP ×2
Metals
_MG ×2
Waters ×165
* Residue conservation analysis
PDB id:
1mc3
Name: Transferase
Title: Crystal structure of rffh
Structure: Glucose-1-phosphate thymidylyltransferase. Chain: a, b. Synonym: rffh, dtdp-glucose synthase, dtdp-glucose pyrophosphorylase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.60Å     R-factor:   0.223     R-free:   0.280
Authors: J.Sivaraman,V.Sauve,A.Matte,M.Cygler,Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)
Key ref:
J.Sivaraman et al. (2002). Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+. J Biol Chem, 277, 44214-44219. PubMed id: 12171937 DOI: 10.1074/jbc.M206932200
Date:
05-Aug-02     Release date:   20-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61887  (RMLA2_ECOLI) -  Glucose-1-phosphate thymidylyltransferase 2
Seq:
Struc:
293 a.a.
291 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 = TTP)
corresponds exactly
+ alpha-D-glucose 1-phosphate
= diphosphate
+ dTDP-alpha-D-glucose
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   5 terms 
  Biochemical function     transferase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M206932200 J Biol Chem 277:44214-44219 (2002)
PubMed id: 12171937  
 
 
Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+.
J.Sivaraman, V.Sauvé, A.Matte, M.Cygler.
 
  ABSTRACT  
 
The enzyme glucose-1-phosphate thymidylyltransferase (RffH), the product of the rffh gene, catalyzes one of the steps in the synthesis of enterobacterial common antigen (ECA), a cell surface glycolipid found in Gram-negative enteric bacteria. In Escherichia coli two gene products, RffH and RmlA, catalyze the same enzymatic reaction and are homologous in sequence; however, they are part of different operons and function in different pathways. We report the crystal structure of RffH bound to deoxythymidine triphosphate (dTTP), the phosphate donor, and Mg(2+), refined at 2.6 A to an R-factor of 22.3% (R(free) = 28.4%). The crystal structure of RffH shows a tetrameric enzyme best described as a dimer of dimers. Each monomer has an overall alpha/beta fold and consists of two domains, a larger nucleotide binding domain (residues 1-115, 222-291) and a smaller sugar-binding domain (116-221), with the active site located at the domain interface. The Mg(2+) ion is coordinated by two conserved aspartates and the alpha-phosphate of deoxythymidine triphosphate. Its location corresponds well to that in a structurally similar domain of N-acetylglucosamine-1-phosphate uridylyltransferase (GlmU). Analysis of the RffH, RmlA, and GlmU complexes with substrates and products provides an explanation for their different affinities for Mg(2+) and leads to a proposal for the dynamics along the reaction pathway.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo view of the tetramer organization of RffH (monomer A, cyan, monomer B, blue; monomers A' and B', green) and its comparison with the tetramer of RmlA from P. aeroginosa (red). The superposition is based on AB dimers and shows a difference in disposition of A' and B' dimers.
Figure 3.
Fig. 3. Stereo view of the dTTP bound to RffH. The hydrogen bonds are shown as red lines. Coordination bonds to the Mg2+ ion are shown in black lines. The electron density at the 3.0 level of the simulated annealing F[o] F[c] omit map, with residues within 3 Å of the dTTP and Mg2+ removed from calculations, is shown in blue lines. Figure was created with Bobscript (26).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 44214-44219) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21370307 J.F.Trempe, S.Shenker, G.Kozlov, and K.Gehring (2011).
Self-association studies of the bifunctional N-acetylglucosamine-1-phosphate uridyltransferase from Escherichia coli.
  Protein Sci, 20, 745-752.  
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
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.  
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
  16946483 D.Aragão, A.R.Marques, C.Frazão, F.J.Enguita, M.A.Carrondo, A.M.Fialho, I.Sá-Correia, and E.P.Mitchell (2006).
Cloning, expression, purification, crystallization and preliminary structure determination of glucose-1-phosphate uridylyltransferase (UgpG) from Sphingomonas elodea ATCC 31461 bound to glucose-1-phosphate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 930-934.  
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.  
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.  
  16511013 J.R.Cupp-Vickery, R.Y.Igarashi, and C.R.Meyer (2005).
Preliminary crystallographic analysis of ADP-glucose pyrophosphorylase from Agrobacterium tumefaciens.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 266-268.  
15692569 X.Jin, M.A.Ballicora, J.Preiss, and J.H.Geiger (2005).
Crystal structure of potato tuber ADP-glucose pyrophosphorylase.
  EMBO J, 24, 694-704.
PDB codes: 1yp2 1yp3 1yp4
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.  
12794190 M.A.Ballicora, A.A.Iglesias, and J.Preiss (2003).
ADP-glucose pyrophosphorylase, a regulatory enzyme for bacterial glycogen synthesis.
  Microbiol Mol Biol Rev, 67, 213.  
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.