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PDBsum entry 1gx0

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1gx0
Jmol
Contents
Protein chains
287 a.a. *
Ligands
UDP ×2
GOL ×2
GAL
Metals
_MN ×2
Waters ×497
* Residue conservation analysis
PDB id:
1gx0
Name: Transferase
Title: Alpha-,1,3 galactosyltransferase - beta-d-galactose complex
Structure: N-acetyllactosaminide alpha-1,3-galactosyltransferase. Chain: a, b. Fragment: catalytic domain, residues 80-368. Synonym: galactosyltransferase, udp-galactose\: beta-d-galactosyl-1,4-n-acetyl-d-glucosaminide alpha-1,3-galactosyltransferase. Engineered: yes
Source: Bos taurus. Bovine. Organism_taxid: 9913. Expressed in: escherichia coli. Expression_system_taxid: 668369. Expression_system_variant: dh5[alpha].
Resolution:
1.80Å     R-factor:   0.189     R-free:   0.211
Authors: E.Boix,Y.Zhang,G.J.Swaminathan,K.Brew,K.R.Acharya
Key ref:
E.Boix et al. (2002). Structural basis of ordered binding of donor and acceptor substrates to the retaining glycosyltransferase, alpha-1,3-galactosyltransferase. J Biol Chem, 277, 28310-28318. PubMed id: 12011052 DOI: 10.1074/jbc.M202631200
Date:
26-Mar-02     Release date:   20-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14769  (GGTA1_BOVIN) -  N-acetyllactosaminide alpha-1,3-galactosyltransferase
Seq:
Struc:
368 a.a.
287 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.87  - N-acetyllactosaminide 3-alpha-galactosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: UDP-alpha-D-galactose + beta-D-galactosyl-(1->4)-beta-N-acetyl-D- glucosaminyl-R = UDP + alpha-D-galactosyl-(1->3)-beta-D-galactosyl- (1->4)-beta-N-acetylglucosaminyl-R
UDP-alpha-D-galactose
+
beta-D-galactosyl-(1->4)-beta-N-acetyl-D- glucosaminyl-R
Bound ligand (Het Group name = GAL)
matches with 44.44% similarity
=
UDP
Bound ligand (Het Group name = UDP)
corresponds exactly
+ alpha-D-galactosyl-(1->3)-beta-D-galactosyl- (1->4)-beta-N-acetylglucosaminyl-R
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     transferase activity, transferring hexosyl groups     1 term  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M202631200 J Biol Chem 277:28310-28318 (2002)
PubMed id: 12011052  
 
 
Structural basis of ordered binding of donor and acceptor substrates to the retaining glycosyltransferase, alpha-1,3-galactosyltransferase.
E.Boix, Y.Zhang, G.J.Swaminathan, K.Brew, K.R.Acharya.
 
  ABSTRACT  
 
Bovine alpha-1,3-galactosyltransferase (alpha3GT) catalyzes the synthesis of the alpha-galactose (alpha-Gal) epitope, the target of natural human antibodies. It represents a family of enzymes, including the histo blood group A and B transferases, that catalyze retaining glycosyltransfer reactions of unknown mechanism. An initial study of alpha3GT in a crystal form with limited resolution and considerable disorder suggested the possible formation of a beta-galactosyl-enzyme covalent intermediate (Gastinel, L. N., Bignon, C., Misra, A. K., Hindsgaul, O., Shaper, J. H., and Joziasse, D. H. (2001) EMBO J. 20, 638-649). Highly ordered structures are described for complexes of alpha3GT with donor substrate, UDP-galactose, UDP- glucose, and two acceptor substrates, lactose and N-acetyllactosamine, at resolutions up to 1.46 A. Structural and calorimetric binding studies suggest an obligatory ordered binding of donor and acceptor substrates, linked to a donor substrate-induced conformational change, and the direct participation of UDP in acceptor binding. The monosaccharide-UDP bond is cleaved in the structures containing UDP-galactose and UDP-glucose, producing non-covalent complexes containing buried beta-galactose and alpha-glucose. The location of these monosaccharides and molecular modeling suggest that binding of a distorted conformation of UDP-galactose may be important in the catalytic mechanism of alpha3GT.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. A, C, E, and G: diagrams of the |F[o]| |F[c]| electron density omit map, contoured at 3.0- level, of LacNAc (1.46 Å), Lac (2.5 Å), -Gal (1.8 Å), and -Glc (1.8 Å), respectively. B, D, F, and H: diagrams showing the interactions of 3GT with LacNAc, lactose, -Gal, and -Glc, respectively. The protein residues are drawn as ball-and-stick models, water molecules appear as blue spheres, and the ligands are shown in orange. The Mn2+ ion is shown as a magenta sphere. H-bonds are indicated by dashed lines. The figures were created with BOBSCRIPT (34).
Figure 4.
Fig. 4. Schematic showing the 3GT residues at the active site and the bound ligands. The Mn2+ ion is shown in magenta, UDP in orange, -Gal in green, and LacNAc in pink. The protein residues are drawn as light gray ball-and-stick models. H-bonds are shown in dashed lines. The figure was created with MOLSCRIPT (33) and rendered using Raster3D (35).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 28310-28318) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20655926 B.Schuman, M.Persson, R.C.Landry, R.Polakowski, J.T.Weadge, N.O.Seto, S.N.Borisova, M.M.Palcic, and S.V.Evans (2010).
Cysteine-to-serine mutants dramatically reorder the active site of human ABO(H) blood group B glycosyltransferase without affecting activity: structural insights into cooperative substrate binding.
  J Mol Biol, 402, 399-411.
PDB codes: 3i0c 3i0d 3i0e 3i0f 3i0g 3i0h 3i0i 3i0j 3i0k 3i0l
21057479 C.J.Bosques, B.E.Collins, J.W.Meador, H.Sarvaiya, J.L.Murphy, G.Dellorusso, D.A.Bulik, I.H.Hsu, N.Washburn, S.F.Sipsey, J.R.Myette, R.Raman, Z.Shriver, R.Sasisekharan, and G.Venkataraman (2010).
Chinese hamster ovary cells can produce galactose-α-1,3-galactose antigens on proteins.
  Nat Biotechnol, 28, 1153-1156.  
20042032 F.Yamamoto, M.Yamamoto, and A.Blancher (2010).
Generation of histo-blood group B transferase by replacing the N-acetyl-d-galactosamine recognition domain of human A transferase with the galactose-recognition domain of evolutionarily related murine alpha1,3-galactosyltransferase.
  Transfusion, 50, 622-630.  
20672277 G.K.Wagner, and T.Pesnot (2010).
Glycosyltransferases and their assays.
  Chembiochem, 11, 1939-1949.  
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 3guh
19845399 S.Liu, L.Meng, K.W.Moremen, and J.H.Prestegard (2009).
Nuclear magnetic resonance structural characterization of substrates bound to the alpha-2,6-sialyltransferase, ST6Gal-I.
  Biochemistry, 48, 11211-11219.  
18047841 B.A.Macher, and U.Galili (2008).
The Galalpha1,3Galbeta1,4GlcNAc-R (alpha-Gal) epitope: a carbohydrate of unique evolution and clinical relevance.
  Biochim Biophys Acta, 1780, 75-88.  
  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.  
  19058170 C.J.Thibodeaux, C.E.Melançon, and H.W.Liu (2008).
Natural-product sugar biosynthesis and enzymatic glycodiversification.
  Angew Chem Int Ed Engl, 47, 9814-9859.  
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.  
18782853 P.Tumbale, H.Jamaluddin, N.Thiyagarajan, K.R.Acharya, and K.Brew (2008).
Screening a limited structure-based library identifies UDP-GalNAc-specific mutants of alpha-1,3-galactosyltransferase.
  Glycobiology, 18, 1036-1043.
PDB codes: 2vxl 2vxm
17850816 A.L.Milac, N.V.Buchete, T.A.Fritz, G.Hummer, and L.A.Tabak (2007).
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2.
  J Mol Biol, 373, 439-451.  
17460661 C.J.Thibodeaux, C.E.Melançon, and H.W.Liu (2007).
Unusual sugar biosynthesis and natural product glycodiversification.
  Nature, 446, 1008-1016.  
17642512 J.A.Letts, M.Persson, B.Schuman, S.N.Borisova, M.M.Palcic, and S.V.Evans (2007).
The effect of heavy atoms on the conformation of the active-site polypeptide loop in human ABO(H) blood-group glycosyltransferase B.
  Acta Crystallogr D Biol Crystallogr, 63, 860-865.
PDB codes: 2pgv 2pgy
17574762 P.Molina, R.M.Knegtel, and B.A.Macher (2007).
Site-directed mutagenesis of glutamate 317 of bovine alpha-1,3Galactosyltransferase and its effect on enzyme activity: implications for reaction mechanism.
  Biochim Biophys Acta, 1770, 1266-1273.  
16715540 A.Valade, D.Urban, and J.M.Beau (2006).
Target-assisted selection of galactosyltransferase binders from dynamic combinatorial libraries. An unexpected solution with restricted amounts of the enzyme.
  Chembiochem, 7, 1023-1027.  
17113856 M.Sobhany, and M.Negishi (2006).
Characterization of specific donor binding to alpha1,4-N-acetylhexosaminyltransferase EXTL2 using isothermal titration calorimetry.
  Methods Enzymol, 416, 3.  
16007668 C.J.Zea, and N.L.Pohl (2005).
Unusual sugar nucleotide recognition elements of mesophilic vs. thermophilic glycogen synthases.
  Biopolymers, 79, 106-113.  
15653326 P.K.Qasba, B.Ramakrishnan, and E.Boeggeman (2005).
Substrate-induced conformational changes in glycosyltransferases.
  Trends Biochem Sci, 30, 53-62.  
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.