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PDBsum entry 2bgu
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Transferase (glycosyltransferase)
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PDB id
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2bgu
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Enzyme class:
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E.C.2.4.1.27
- Dna beta-glucosyltransferase.
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Reaction:
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Transfers a beta-D-glucosyl residue from UDP-glucose to an hydroxymethylcytosine residue in DNA.
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Embo J
13:3413-3422
(1994)
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PubMed id:
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Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
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A.Vrielink,
W.Rüger,
H.P.Driessen,
P.S.Freemont.
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ABSTRACT
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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.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.Dahl,
K.Grønbæk,
and
P.Guldberg
(2011).
Advances in DNA methylation: 5-hydroxymethylcytosine revisited.
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Clin Chim Acta,
412,
831-836.
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G.K.Wagner,
and
T.Pesnot
(2010).
Glycosyltransferases and their assays.
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Chembiochem,
11,
1939-1949.
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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.
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Chem Biol,
16,
676-685.
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PDB codes:
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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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J Biol Chem,
284,
3294-3305.
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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.
|
| |
J Biol Chem,
284,
21613-21625.
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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.
|
| |
Protein Eng Des Sel,
21,
537-543.
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B.Henrissat,
G.Sulzenbacher,
and
Y.Bourne
(2008).
Glycosyltransferases, glycoside hydrolases: surprise, surprise!
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| |
Curr Opin Struct Biol,
18,
527-533.
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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.
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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.
|
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Chem Cent J,
2,
15.
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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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J Bacteriol,
190,
4922-4932.
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L.L.Lairson,
B.Henrissat,
G.J.Davies,
and
S.G.Withers
(2008).
Glycosyltransferases: structures, functions, and mechanisms.
|
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Annu Rev Biochem,
77,
521-555.
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M.Barreras,
S.R.Salinas,
P.L.Abdian,
M.A.Kampel,
and
L.Ielpi
(2008).
Structure and Mechanism of GumK, a Membrane-associated Glucuronosyltransferase.
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J Biol Chem,
283,
25027-25035.
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PDB codes:
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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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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
1121-1124.
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C.Hertweck,
A.Luzhetskyy,
Y.Rebets,
and
A.Bechthold
(2007).
Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork.
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Nat Prod Rep,
24,
162-190.
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H.Y.Sun,
S.W.Lin,
T.P.Ko,
J.F.Pan,
C.L.Liu,
C.N.Lin,
A.H.Wang,
and
C.H.Lin
(2007).
Structure and mechanism of Helicobacter pylori fucosyltransferase. A basis for lipopolysaccharide variation and inhibitor design.
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J Biol Chem,
282,
9973-9982.
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PDB codes:
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J.Bischerour,
and
R.Chalmers
(2007).
Base-flipping dynamics in a DNA hairpin processing reaction.
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Nucleic Acids Res,
35,
2584-2595.
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M.J.Miley,
A.K.Zielinska,
J.E.Keenan,
S.M.Bratton,
A.Radominska-Pandya,
and
M.R.Redinbo
(2007).
Crystal structure of the cofactor-binding domain of the human phase II drug-metabolism enzyme UDP-glucuronosyltransferase 2B7.
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J Mol Biol,
369,
498-511.
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PDB code:
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R.B.Russell
(2007).
Classification of protein folds.
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Mol Biotechnol,
36,
238-247.
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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.
|
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
142-144.
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H.Merzendorfer
(2006).
Insect chitin synthases: a review.
|
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J Comp Physiol [B],
176,
1.
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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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EMBO J,
25,
1396-1405.
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PDB codes:
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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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Mol Biosyst,
1,
117-126.
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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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J Biol Chem,
280,
35537-35544.
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C.J.Zea,
and
N.L.Pohl
(2005).
Unusual sugar nucleotide recognition elements of mesophilic vs. thermophilic glycogen synthases.
|
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Biopolymers,
79,
106-113.
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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.
|
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Nat Struct Mol Biol,
12,
608-614.
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PDB codes:
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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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EMBO J,
23,
3196-3205.
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PDB codes:
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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.
|
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Nat Struct Mol Biol,
11,
163-170.
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PDB codes:
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L.Larivière,
and
S.Moréra
(2004).
Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase.
|
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J Biol Chem,
279,
34715-34720.
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PDB codes:
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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.
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PDB codes:
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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.
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PDB codes:
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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.
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E.S.Miller,
E.Kutter,
G.Mosig,
F.Arisaka,
T.Kunisawa,
and
W.Rüger
(2003).
Bacteriophage T4 genome.
|
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Microbiol Mol Biol Rev,
67,
86.
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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.
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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.
|
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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.
|
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J Biol Chem,
278,
45864-45881.
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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.
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Proc Natl Acad Sci U S A,
100,
845-849.
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PDB code:
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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.
|
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Biochemistry,
41,
6824-6833.
|
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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.
|
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Acta Crystallogr D Biol Crystallogr,
58,
1484-1486.
|
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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).
|
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Eur J Biochem,
269,
4308-4316.
|
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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.
|
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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.
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PDB codes:
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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.
|
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Chem Biol,
8,
557-567.
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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.
|
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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.
|
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PDB codes:
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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.
|
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|
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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.
|
|
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|
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|
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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.
|
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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.
|
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Y.Bourne,
and
B.Henrissat
(2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
|
| |
Curr Opin Struct Biol,
11,
593-600.
|
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|
|
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|
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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.
|
|
|
|
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|
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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.
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PDB code:
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U.M.Unligil,
and
J.M.Rini
(2000).
Glycosyltransferase structure and mechanism.
|
| |
Curr Opin Struct Biol,
10,
510-517.
|
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|
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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.
|
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PDB codes:
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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.
|
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C.Breton,
and
A.Imberty
(1999).
Structure/function studies of glycosyltransferases.
|
| |
Curr Opin Struct Biol,
9,
563-571.
|
|
|
|
|
|
|
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.
|
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|
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H.D.Ly,
and
S.G.Withers
(1999).
Mutagenesis of glycosidases.
|
| |
Annu Rev Biochem,
68,
487-522.
|
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|
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H.K.Song,
S.H.Sohn,
and
S.W.Suh
(1999).
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PDB code:
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The most recent references are shown first.
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only a partial list as not all journals are covered by
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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.
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