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PDBsum entry 1bgu

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Transferase(glucosyltransferase) PDB id
1bgu
Jmol
Contents
Protein chain
328 a.a.*
Ligands
UDP
* C-alpha coords only
PDB id:
1bgu
Name: Transferase(glucosyltransferase)
Title: Crystal structure of the DNA modifying enzyme beta- glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose
Structure: Beta-glucosyltransferase. Chain: a. Engineered: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665
Resolution:
2.20Å     R-factor:   0.191    
Authors: A.Vrielink,W.Rueger,H.P.C.Driessen,P.S.Freemont
Key ref: A.Vrielink et al. (1994). Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose. EMBO J, 13, 3413-3422. PubMed id: 8062817
Date:
09-Jun-94     Release date:   15-Oct-94    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04547  (GSTB_BPT4) -  DNA beta-glucosyltransferase
Seq:
Struc:
351 a.a.
328 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.27  - Dna beta-glucosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Transfers a beta-D-glucosyl residue from UDP-glucose to an hydroxymethylcytosine residue in DNA.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     viral reproduction   2 terms 
  Biochemical function     transferase activity     3 terms  

 

 
EMBO J 13:3413-3422 (1994)
PubMed id: 8062817  
 
 
Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
A.Vrielink, W.Rüger, H.P.Driessen, P.S.Freemont.
 
  ABSTRACT  
 
Bacteriophage T4 beta-glucosyltransferase (EC 2.4.1.27) catalyses the transfer of glucose from uridine diphosphoglucose to hydroxymethyl groups of modified cytosine bases in T4 duplex DNA forming beta-glycosidic linkages. The enzyme forms part of a phage DNA protection system. We have solved and refined the crystal structure of recombinant beta-glucosyltransferase to 2.2 A resolution in the presence and absence of the substrate, uridine diphosphoglucose. The structure comprises two domains of similar topology, each reminiscent of a nucleotide binding fold. The two domains are separated by a central cleft which generates a concave surface along one side of the molecule. The substrate-bound complex reveals only clear electron density for the uridine diphosphate portion of the substrate. The UDPG is bound in a pocket at the bottom of the cleft between the two domains and makes extensive hydrogen bonding contacts with residues of the C-terminal domain only. The domains undergo a rigid body conformational change causing the structure to adopt a more closed conformation upon ligand binding. The movement of the domains is facilitated by a hinge region between residues 166 and 172. Electrostatic surface potential calculations reveal a large positive potential along the concave surface of the structure, suggesting a possible site for duplex DNA interaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21324307 C.Dahl, K.Grønbæk, and P.Guldberg (2011).
Advances in DNA methylation: 5-hydroxymethylcytosine revisited.
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19549605 A.W.Truman, M.V.Dias, S.Wu, T.L.Blundell, F.Huang, and J.B.Spencer (2009).
Chimeric glycosyltransferases for the generation of hybrid glycopeptides.
  Chem Biol, 16, 676-685.
PDB codes: 3h4i 3h4t
19028689 K.B.Luther, H.Schindelin, and R.S.Haltiwanger (2009).
Structural and mechanistic insights into lunatic fringe from a kinetic analysis of enzyme mutants.
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19520856 M.E.Guerin, F.Schaeffer, A.Chaffotte, P.Gest, D.Giganti, J.Korduláková, M.van der Woerd, M.Jackson, and P.M.Alzari (2009).
Substrate-induced Conformational Changes in the Essential Peripheral Membrane-associated Mannosyltransferase PimA from Mycobacteria: IMPLICATIONS FOR CATALYSIS.
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18502788 A.S.Patana, M.Kurkela, M.Finel, and A.Goldman (2008).
Mutation analysis in UGT1A9 suggests a relationship between substrate and catalytic residues in UDP-glucuronosyltransferases.
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18822375 B.Henrissat, G.Sulzenbacher, and Y.Bourne (2008).
Glycosyltransferases, glycoside hydrolases: surprise, surprise!
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Thermodynamics of binding of divalent magnesium and manganese to uridine phosphates: implications for diabetes-related hypomagnesaemia and carbohydrate biocatalysis.
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18487334 I.Brockhausen, B.Hu, B.Liu, K.Lau, W.A.Szarek, L.Wang, and L.Feng (2008).
Characterization of two beta-1,3-glucosyltransferases from Escherichia coli serotypes O56 and O152.
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18518825 L.L.Lairson, B.Henrissat, G.J.Davies, and S.G.Withers (2008).
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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
  19052364 P.Gest, D.Kaur, H.T.Pham, M.van der Woerd, E.Hansen, P.J.Brennan, M.Jackson, and M.E.Guerin (2008).
Preliminary crystallographic analysis of GpgS, a key glucosyltransferase involved in methylglucose lipopolysaccharide biosynthesis in Mycobacterium tuberculosis.
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17268612 C.Hertweck, A.Luzhetskyy, Y.Rebets, and A.Bechthold (2007).
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Structure and mechanism of Helicobacter pylori fucosyltransferase. A basis for lipopolysaccharide variation and inhibitor design.
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PDB codes: 2nzw 2nzx 2nzy
17412704 J.Bischerour, and R.Chalmers (2007).
Base-flipping dynamics in a DNA hairpin processing reaction.
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Crystal structure of the cofactor-binding domain of the human phase II drug-metabolism enzyme UDP-glucuronosyltransferase 2B7.
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PDB code: 2o6l
17873410 R.B.Russell (2007).
Classification of protein folds.
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  16511286 D.U.Kim, J.H.Yoo, K.Ryu, and H.S.Cho (2006).
Crystallization and preliminary X-ray crystallographic analysis of the alpha-2,6-sialyltransferase PM0188 from Pasteurella multosida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 142-144.  
16075270 H.Merzendorfer (2006).
Insect chitin synthases: a review.
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16482224 W.Offen, C.Martinez-Fleites, M.Yang, E.Kiat-Lim, B.G.Davis, C.A.Tarling, C.M.Ford, D.J.Bowles, and G.J.Davies (2006).
Structure of a flavonoid glucosyltransferase reveals the basis for plant natural product modification.
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PDB codes: 2c1x 2c1z 2c9z
16880973 A.Luzhetskyy, A.Vente, and A.Bechthold (2005).
Glycosyltransferases involved in the biosynthesis of biologically active natural products that contain oligosaccharides.
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16105839 B.D.Lazarus, M.D.Roos, and J.A.Hanover (2005).
Mutational analysis of the catalytic domain of O-linked N-acetylglucosaminyl transferase.
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16007668 C.J.Zea, and N.L.Pohl (2005).
Unusual sugar nucleotide recognition elements of mesophilic vs. thermophilic glycogen synthases.
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15951819 J.Flint, E.Taylor, M.Yang, D.N.Bolam, L.E.Tailford, C.Martinez-Fleites, E.J.Dodson, B.G.Davis, H.J.Gilbert, and G.J.Davies (2005).
Structural dissection and high-throughput screening of mannosylglycerate synthase.
  Nat Struct Mol Biol, 12, 608-614.
PDB codes: 2bo4 2bo6 2bo7 2bo8
15272305 A.Buschiazzo, J.E.Ugalde, M.E.Guerin, W.Shepard, R.A.Ugalde, and P.M.Alzari (2004).
Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation.
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PDB codes: 1rzu 1rzv
14730352 C.P.Chiu, A.G.Watts, L.L.Lairson, M.Gilbert, D.Lim, W.W.Wakarchuk, S.G.Withers, and N.C.Strynadka (2004).
Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog.
  Nat Struct Mol Biol, 11, 163-170.
PDB codes: 1ro7 1ro8
15178685 L.Larivière, and S.Moréra (2004).
Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase.
  J Biol Chem, 279, 34715-34720.
PDB codes: 1sxp 1sxq
14570926 R.P.Gibson, C.A.Tarling, S.Roberts, S.G.Withers, and G.J.Davies (2004).
The donor subsite of trehalose-6-phosphate synthase: binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 A resolution.
  J Biol Chem, 279, 1950-1955.
PDB codes: 1uqt 1uqu
12874381 A.M.Mulichak, H.C.Losey, W.Lu, Z.Wawrzak, C.T.Walsh, and R.M.Garavito (2003).
Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway.
  Proc Natl Acad Sci U S A, 100, 9238-9243.
PDB codes: 1pn3 1pnv
14646108 C.Horcajada, E.Cid, J.J.Guinovart, N.Verdaguer, and J.C.Ferrer (2003).
Crystallization and preliminary X-ray analysis of the glycogen synthase from Pyrococcus abyssi.
  Acta Crystallogr D Biol Crystallogr, 59, 2322-2324.  
12626685 E.S.Miller, E.Kutter, G.Mosig, F.Arisaka, T.Kunisawa, and W.Rüger (2003).
Bacteriophage T4 genome.
  Microbiol Mol Biol Rev, 67, 86.  
12464611 M.Edman, S.Berg, P.Storm, M.Wikström, S.Vikström, A.Ohman, and A.Wieslander (2003).
Structural features of glycosyltransferases synthesizing major bilayer and nonbilayer-prone membrane lipids in Acholeplasma laidlawii and Streptococcus pneumoniae.
  J Biol Chem, 278, 8420-8428.  
12803927 T.D.Butters, H.R.Mellor, K.Narita, R.A.Dwek, and F.M.Platt (2003).
Small-molecule therapeutics for the treatment of glycolipid lysosomal storage disorders.
  Philos Trans R Soc Lond B Biol Sci, 358, 927-945.  
12954635 T.Y.Yen, B.A.Macher, S.Bryson, X.Chang, I.Tvaroska, R.Tse, S.Takeshita, A.M.Lew, and A.Datti (2003).
Highly conserved cysteines of mouse core 2 beta1,6-N-acetylglucosaminyltransferase I form a network of disulfide bonds and include a thiol that affects enzyme activity.
  J Biol Chem, 278, 45864-45881.  
12538870 Y.Hu, L.Chen, S.Ha, B.Gross, B.Falcone, D.Walker, M.Mokhtarzadeh, and S.Walker (2003).
Crystal structure of the MurG:UDP-GlcNAc complex reveals common structural principles of a superfamily of glycosyltransferases.
  Proc Natl Acad Sci U S A, 100, 845-849.
PDB code: 1nlm
12022887 L.Chen, H.Men, S.Ha, X.Y.Ye, L.Brunner, Y.Hu, and S.Walker (2002).
Intrinsic lipid preferences and kinetic mechanism of Escherichia coli MurG.
  Biochemistry, 41, 6824-6833.  
12198310 L.Larivière, J.Kurzeck, U.Aschke-Sonnenborn, W.Rüger, and S.Moréra (2002).
Crystallization and preliminary crystallographic study of a ternary complex between the T4 phage beta-glucosyltransferase, uridine diphosphoglucose and a DNA fragment containing an abasic site.
  Acta Crystallogr D Biol Crystallogr, 58, 1484-1486.  
12199709 M.Tenno, S.Toba, F.J.Kézdy, A.P.Elhammer, and A.Kurosaka (2002).
Identification of two cysteine residues involved in the binding of UDP-GalNAc to UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1).
  Eur J Biochem, 269, 4308-4316.  
11807274 R.P.Gibson, R.M.Lloyd, S.J.Charnock, and G.J.Davies (2002).
Characterization of Escherichia coli OtsA, a trehalose-6-phosphate synthase from glycosyltransferase family 20.
  Acta Crystallogr D Biol Crystallogr, 58, 349-351.  
12198488 S.I.Patenaude, N.O.Seto, S.N.Borisova, A.Szpacenko, S.L.Marcus, M.M.Palcic, and S.V.Evans (2002).
The structural basis for specificity in human ABO(H) blood group biosynthesis.
  Nat Struct Biol, 9, 685-690.
PDB codes: 1lz0 1lz7 1lzi 1lzj
11410375 D.Hoffmeister, K.Ichinose, and A.Bechthold (2001).
Two sequence elements of glycosyltransferases involved in urdamycin biosynthesis are responsible for substrate specificity and enzymatic activity.
  Chem Biol, 8, 557-567.  
11398978 E.J.Hehre (2001).
Glycosyl transfer: a history of the concept's development and view of its major contributions to biochemistry.
  Carbohydr Res, 331, 347-368.  
11179209 L.N.Gastinel, C.Bignon, A.K.Misra, O.Hindsgaul, J.H.Shaper, and D.H.Joziasse (2001).
Bovine alpha1,3-galactosyltransferase catalytic domain structure and its relationship with ABO histo-blood group and glycosphingolipid glycosyltransferases.
  EMBO J, 20, 638-649.
PDB codes: 1fg5 1g8o 1g93
11484220 M.Rao, and I.Tvaroska (2001).
Structure of bovine alpha-1,3-galactosyltransferase and its complexes with UDP and DPGal inferred from molecular modeling.
  Proteins, 44, 428-434.  
11285558 P.Petrová, C.Monteiro, C.Hervé du Penhoat, J.Koca, and A.Imberty (2001).
Conformational behavior of nucleotide-sugar in solution: molecular dynamics and NMR study of solvated uridine diphosphate-glucose in the presence of monovalent cations.
  Biopolymers, 58, 617-635.  
11717264 V.Chazalet, K.Uehara, R.A.Geremia, and C.Breton (2001).
Identification of essential amino acids in the Azorhizobium caulinodans fucosyltransferase NodZ.
  J Bacteriol, 183, 7067-7075.  
11114903 W.J.Keenleyside, A.J.Clarke, and C.Whitfield (2001).
Identification of residues involved in catalytic activity of the inverting glycosyl transferase WbbE from Salmonella enterica serovar borreze.
  J Bacteriol, 183, 77-85.  
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
10811884 A.Vanderplasschen, N.Markine-Goriaynoff, P.Lomonte, M.Suzuki, N.Hiraoka, J.C.Yeh, F.Bureau, L.Willems, E.Thiry, M.Fukuda, and P.P.Pastoret (2000).
A multipotential beta -1,6-N-acetylglucosaminyl-transferase is encoded by bovine herpesvirus type 4.
  Proc Natl Acad Sci U S A, 97, 5756-5761.  
  10892798 S.Ha, D.Walker, Y.Shi, and S.Walker (2000).
The 1.9 A crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis.
  Protein Sci, 9, 1045-1052.
PDB code: 1f0k
11042447 U.M.Unligil, and J.M.Rini (2000).
Glycosyltransferase structure and mechanism.
  Curr Opin Struct Biol, 10, 510-517.  
11032794 U.M.Unligil, S.Zhou, S.Yuwaraj, M.Sarkar, H.Schachter, and J.M.Rini (2000).
X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
  EMBO J, 19, 5269-5280.
PDB codes: 1fo8 1fo9 1foa
10608830 B.Lougheed, H.D.Ly, W.W.Wakarchuk, and S.G.Withers (1999).
Glycosyl fluorides can function as substrates for nucleotide phosphosugar-dependent glycosyltransferases.
  J Biol Chem, 274, 37717-37722.  
10508766 C.Breton, and A.Imberty (1999).
Structure/function studies of glycosyltransferases.
  Curr Opin Struct Biol, 9, 563-571.  
10037781 F.K.Hagen, B.Hazes, R.Raffo, D.deSa, and L.A.Tabak (1999).
Structure-function analysis of the UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase. Essential residues lie in a predicted active site cleft resembling a lactose repressor fold.
  J Biol Chem, 274, 6797-6803.  
10872458 H.D.Ly, and S.G.Withers (1999).
Mutagenesis of glycosidases.
  Annu Rev Biochem, 68, 487-522.  
10064578 H.K.Song, S.H.Sohn, and S.W.Suh (1999).
Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex.
  EMBO J, 18, 1104-1113.
PDB codes: 1b49 1b5d 1b5e
10393171 L.N.Gastinel, C.Cambillau, and Y.Bourne (1999).
Crystal structures of the bovine beta4galactosyltransferase catalytic domain and its complex with uridine diphosphogalactose.
  EMBO J, 18, 3546-3557.
PDB codes: 1fgx 1fr8
10092863 N.O.Seto, C.A.Compston, S.V.Evans, D.R.Bundle, S.A.Narang, and M.M.Palcic (1999).
Donor substrate specificity of recombinant human blood group A, B and hybrid A/B glycosyltransferases expressed in Escherichia coli.
  Eur J Biochem, 259, 770-775.  
9461471 B.Holz, S.Klimasauskas, S.Serva, and E.Weinhold (1998).
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
  Nucleic Acids Res, 26, 1076-1083.  
9653120 C.A.Wiggins, and S.Munro (1998).
Activity of the yeast MNN1 alpha-1,3-mannosyltransferase requires a motif conserved in many other families of glycosyltransferases.
  Proc Natl Acad Sci U S A, 95, 7945-7950.  
9759487 R.J.Roberts, and X.Cheng (1998).
Base flipping.
  Annu Rev Biochem, 67, 181-198.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
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9007278 T.Endo, Y.Kajihara, H.Kodama, and H.Hashimoto (1996).
Novel aspects of interaction between UDP-gal and GlcNAc beta-1,4-galactosyltransferase: transferability and remarkable inhibitory activity of UDP-(mono-O-methylated gal), UDP-Fuc and UDP-man.
  Bioorg Med Chem, 4, 1939-1948.  
  7670379 K.C.Chou (1995).
A sequence-coupled vector-projection model for predicting the specificity of GalNAc-transferase.
  Protein Sci, 4, 1365-1383.  
  7729407 L.Holm, and C.Sander (1995).
Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme.
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7749914 P.J.Artymiuk, D.W.Rice, A.R.Poirrette, and P.Willett (1995).
beta-Glucosyltransferase and phosphorylase reveal their common theme.
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7606789 R.J.Roberts (1995).
On base flipping.
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7552726 T.E.Benson, D.J.Filman, C.T.Walsh, and J.M.Hogle (1995).
An enzyme-substrate complex involved in bacterial cell wall biosynthesis.
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PDB code: 1mbr
7773746 X.Cheng (1995).
DNA modification by methyltransferases.
  Curr Opin Struct Biol, 5, 4.  
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.