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Transferase PDB-id
2iuy
Biological unit = asymmetric unit, as shown
(as defined in PDB file)
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Protein chains
340 a.a. *
Ligands
MES ×2
SO4 ×2
Waters ×440

* Residue conservation analysis
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PDB id: 2iuy
Name: Transferase
Title: Crystal structure of avigt4, a glycosyltransferase involved in avilamycin a biosynthesis

Structure:
Glycosyltransferase. Chain: a, b. Synonym: avigt4. Engineered: yes

Source:
Streptomyces viridochromogenes. Organism_taxid: 1938. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: dsm 40721

Biological unit:
Monomer (from PDB file)

UniProt:
Chains A, B: Q93KV2 (Q93KV2_STRVR)
Pfam  
Seq:
Struc:
Seq: 342 a.a.
Struc: 340 a.a.
Key:    PfamA domain  Secondary structure

Resolution:
2.1Å

R-factor:
0.173

R-free:
0.233

Authors:
C.Martinez-Fleites,M.Proctor,S.Roberts,D.N.Bolam, H.J.Gilbert,G.J.Davies

Key ref:
C.Martinez-Fleites et al. (2006). Insights into the synthesis of lipopolysaccharide and antibiotics through the structures of two retaining glycosyltransferases from family GT4.. Chem Biol, 13, 1143-1152. [PubMed id: 17113996] [DOI: 10.1016/j.chembiol.2006.09.005]

Date:
08-Jun-06

Release date:
11-Oct-06

Related entries:
2iv3 crystal structure of avigt4, a glycosyltransferase involved in avilamycin a biosynthesis
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    Key reference    
 
 
DOI no: 10.1016/j.chembiol.2006.09.005 Chem Biol 13:1143-1152 (2006)
PubMed id: 17113996  
 
 
Insights into the synthesis of lipopolysaccharide and antibiotics through the structures of two retaining glycosyltransferases from family GT4.
C.Martinez-Fleites, M.Proctor, S.Roberts, D.N.Bolam, H.J.Gilbert, G.J.Davies.
 
  ABSTRACT  
 
Glycosyltransferases (GTs) catalyze the synthesis of the myriad glycoconjugates that are central to life. One of the largest families is GT4, which contains several enzymes of therapeutic significance, exemplified by WaaG and AviGT4. WaaG catalyses a key step in lipopolysaccharide synthesis, while AviGT4, produced by Streptomyces viridochromogenes, contributes to the synthesis of the antibiotic avilamycin A. Here we present the crystal structure of both WaaG and AviGT4. The two enzymes contain two "Rossmann-like" (beta/alpha/beta) domains characteristic of the GT-B fold. Both recognition of the donor substrate and the catalytic machinery is similar to other retaining GTs that display the GT-B fold. Structural information is discussed with respect to the evolution of GTs and the therapeutic significance of the two enzymes.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Catalytic Action of Two Family GT4 GTs
(A) Schematic diagram of E. coli LPS. GlcN, D-glucosamine; Hep, L-glycero-D-manno-heptose; P, phosphate; EtNP, 2-aminoethyl phosphate; Glc, D-glucose; Gal, D-galactose. WaaG is responsible for the addition of the first glucose moiety via an α-1,3 glycosidic linkage to Hep II.
(B) Structure of the antibiotic avilamycin A. Disruption of the avigt4 gene results in a product lacking the eurekanate moiety (boxed) normally bonded to the L-lyxose residue [8].
Figure 5.
Figure 5. Electrostatic Surface Figures of WaaG and AviGT4
Surface representation of (A) WaaG and (B) AviGT4 colored by electrostatic potential (red, −3kT; blue +3kT, where k is the Boltzmann constant and T is temperature), calculated by the Adaptive Poisson-Boltzmann Solver (APBS) program [44] and visualized with Pymol (DeLano Scientific LLC, http://pymol.sourceforge.net/); ligands are shown in licorice representation.
 
  The above figures are reprinted by permission from Cell Press: Chem Biol (2006, 13, 1143-1152) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19233921 A.Ramos, C.Olano, A.F.Braña, C.Méndez, and J.A.Salas (2009).
Modulation of deoxysugar transfer by the elloramycin glycosyltransferase ElmGT through site-directed mutagenesis.
  J Bacteriol, 191, 2871-2875.  
19244233 F.Sheng, X.Jia, A.Yep, J.Preiss, and J.H.Geiger (2009).
The crystal structures of the open and catalytically competent closed conformation of Escherichia coli glycogen synthase.
  J Biol Chem, 284, 17796-17807.
PDB codes: 2qzs 2r4t 2r4u 3cop 3d1j
19170877 H.Claus, K.Stummeyer, J.Batzilla, M.Mühlenhoff, and U.Vogel (2009).
Amino acid 310 determines the donor substrate specificity of serogroup W-135 and Y capsule polymerases of Neisseria meningitidis.
  Mol Microbiol, 71, 960-971.  
18205830 C.Goedl, and B.Nidetzky (2008).
The phosphate site of trehalose phosphorylase from Schizophyllum commune probed by site-directed mutagenesis and chemical rescue studies.
  FEBS J, 275, 903-913.  
18712829 K.M.Ruane, G.J.Davies, and C.Martinez-Fleites (2008).
Crystal structure of a family GT4 glycosyltransferase from Bacillus anthracis ORF BA1558.
  Proteins, 73, 784-787.
PDB code: 2jjm
18311744 K.Yokoyama, Y.Yamamoto, F.Kudo, and T.Eguchi (2008).
Involvement of two distinct N-acetylglucosaminyltransferases and a dual-function deacetylase in neomycin biosynthesis.
  Chembiochem, 9, 865-869.  
18518825 L.L.Lairson, B.Henrissat, G.J.Davies, and S.G.Withers (2008).
Glycosyltransferases: structures, functions, and mechanisms.
  Annu Rev Biochem, 77, 521-555.  
18596046 M.Barreras, S.R.Salinas, P.L.Abdian, M.A.Kampel, and L.Ielpi (2008).
Structure and Mechanism of GumK, a Membrane-associated Glucuronosyltransferase.
  J Biol Chem, 283, 25027-25035.
PDB codes: 2hy7 2q6v 3cuy 3cv3
18390549 M.W.Vetting, P.A.Frantom, and J.S.Blanchard (2008).
Structural and enzymatic analysis of MshA from Corynebacterium glutamicum: substrate-assisted catalysis.
  J Biol Chem, 283, 15834-15844.
PDB codes: 3c48 3c4q 3c4v
18826412 Y.Li, Y.Chen, X.Huang, M.Zhou, R.Wu, S.Dong, D.G.Pritchard, P.Fives-Taylor, and H.Wu (2008).
A conserved domain of previously unknown function in Gap1 mediates protein-protein interaction and is required for biogenesis of a serine-rich streptococcal adhesin.
  Mol Microbiol, 70, 1094-1104.  
18667419 Z.Fulton, A.McAlister, M.C.Wilce, R.Brammananth, L.Zaker-Tabrizi, M.A.Perugini, S.P.Bottomley, R.L.Coppel, P.K.Crellin, J.Rossjohn, and T.Beddoe (2008).
Crystal Structure of a UDP-glucose-specific Glycosyltransferase from a Mycobacterium Species.
  J Biol Chem, 283, 27881-27890.
PDB codes: 3ckj 3ckn 3cko 3ckq 3ckv
17510062 M.E.Guerin, J.Kordulakova, F.Schaeffer, Z.Svetlikova, A.Buschiazzo, D.Giganti, B.Gicquel, K.Mikusova, M.Jackson, and P.M.Alzari (2007).
Molecular recognition and interfacial catalysis by the essential phosphatidylinositol mannosyltransferase PimA from mycobacteria.
  J Biol Chem, 282, 20705-20714.  
17697098 M.L.Klement, L.Ojemyr, K.E.Tagscherer, G.Widmalm, and A.Wieslander (2007).
A processive lipid glycosyltransferase in the small human pathogen Mycoplasma pneumoniae: involvement in host immune response.
  Mol Microbiol, 65, 1444-1457.  
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.