PDBsum entry: 1iir

Transferase

PDB-id

1iir

Contents

Description

Header details

Protein chain

Ligands

SO4

Metal ions

_MG ×2

Waters ×293

* Residue conservation analysis

Tools

Image Generation

AstexViewer™@PDBe

Run PROCHECK

Clefts Calculation

PDB id:

1iir

Name:

Transferase

Title:

Crystal structure of udp-glucosyltransferase gtfb

Structure:

Glycosyltransferase gtfb. Chain: a. Synonym: udp-glycosyltransferase gtfb. Engineered: yes

Source:

Amycolatopsis orientalis. Organism_taxid: 31958. Strain: a82846. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

UniProt:

P96559 (P96559_AMYOR)

Seq:

Struc:

Seq:

407 a.a.

Struc:

382 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Resolution:

1.80Å

R-factor:

0.211

R-free:

0.231

Authors:

A.M.Mulichak,H.C.Losey,C.T.Walsh,R.M.Garavito

Key ref:

A.M.Mulichak et al. (2001). Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics.. Structure, 9, 547-557. [PubMed id: 11470430] [DOI: 10.1016/S0969-2126(01)00616-5]

Date:

24-Apr-01

Release date:

18-Jul-01

Quick_links

RCSB

PDBe

SRS

MMDB

JenaLib

OCA

Proteopedia

CATH

SCOP

FSSP

HSSP

PDBSWS

PQS

ProSAT

Whatcheck

EDS

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/S0969-2126(01)00616-5 Structure 9:547-557 (2001)

PubMed id: 11470430

Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics.

A.M.Mulichak, H.C.Losey, C.T.Walsh, R.M.Garavito.

ABSTRACT

BACKGROUND: Members of the vancomycin group of glycopeptide antibiotics have an oxidatively crosslinked heptapeptide scaffold decorated at the hydroxyl groups of 4-OH-Phegly4 or beta-OH-Tyr6 with mono- (residue 6) or disaccharides (residue 4). The disaccharide in vancomycin itself is L-vancosamine-1,2-glucose, and in chloroeremomycin it is L-4-epi-vancosamine-1,2-glucose. The sugars and their substituents play an important role in efficacy, particularly against vancomycin-resistant pathogenic enterococci. RESULTS: The glucosyltransferase, GtfB, that transfers the glucose residue from UDP-glucose to the 4-OH-Phegly4 residue of the vancomycin aglycone, initiating the glycosylation pathway in chloroeremomycin maturation, has been crystallized, and its structure has been determined by X-ray analysis at 1.8 A resolution. The enzyme has a two-domain structure, with a deep interdomain cleft identified as the likely site of UDP-glucose binding. A hydrophobic patch on the surface of the N-terminal domain is proposed to be the binding site of the aglycone substrate. Mutagenesis has revealed Asp332 as the best candidate for the general base in the glucosyltransfer reaction. CONCLUSIONS: The structure of GtfB places it in a growing group of glycosyltransferases, including Escherichia coli MurG and a beta-glucosyltransferase from T4 phage, which together form a subclass of the glycosyltransferase superfamily and give insights into the recognition of the NDP-sugar and aglycone cosubstrates. A single major interdomain linker between the N- and C- terminal domains suggests that reprogramming of sugar transfer or aglycone recognition in the antibiotic glycosyltransferases, including the glycopeptide and also the macrolide antibiotics, will be facilitated by this structural information.

Selected figure(s)

Figure 4.
Figure 4. Stereo View Showing Ribbon Diagrams of Homologous GtfB, MurG, and T4 b-GT StructuresA high degree of conservation of the b sheets (highlighted in blue) is clearly visible. In the T4 b-GT structure, the bound UDP is shown in red

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 547-557) copyright 2001.

Figure was selected by the author.

Literature references that cite this PDB file's key reference

PubMed id Reference

19636447 A.Koglin, and C.T.Walsh (2009).
Structural insights into nonribosomal peptide enzymatic assembly lines.

Nat Prod Rep, 26, 987.

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.

18985617 S.H.Park, H.Y.Park, J.K.Sohng, H.C.Lee, K.Liou, Y.J.Yoon, and B.G.Kim (2009).
Expanding substrate specificity of GT-B fold glycosyltransferase via domain swapping and high-throughput screening.

Biotechnol Bioeng, 102, 988-994.

19126547 Y.L.Chen, Y.H.Chen, Y.C.Lin, K.C.Tsai, and H.T.Chiu (2009).
Functional characterization and substrate specificity of spinosyn rhamnosyltransferase by in vitro reconstitution of spinosyn biosynthetic enzymes.

J Biol Chem, 284, 7352-7363.

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.

Protein Eng Des Sel, 21, 537-543.

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.

17268612 C.Hertweck, A.Luzhetskyy, Y.Rebets, and A.Bechthold (2007).
Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork.

Nat Prod Rep, 24, 162-190.

17460661 C.J.Thibodeaux, C.E.Melançon, and H.W.Liu (2007).
Unusual sugar biosynthesis and natural product glycodiversification.

Nature, 446, 1008-1016.

17475008 C.Li, and Q.Wu (2007).
Adaptive evolution of multiple-variable exons and structural diversity of drug-metabolizing enzymes.

BMC Evol Biol, 7, 69.

17956868 D.Li, S.Fournel-Gigleux, L.Barré, G.Mulliert, P.Netter, J.Magdalou, and M.Ouzzine (2007).
Identification of aspartic acid and histidine residues mediating the reaction mechanism and the substrate specificity of the human UDP-glucuronosyltransferases 1A.

J Biol Chem, 282, 36514-36524.

17334710 D.Liang, and J.Qiao (2007).
Phylogenetic analysis of antibiotic glycosyltransferases.

J Mol Evol, 64, 342-353.

17251184 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.

J Biol Chem, 282, 9973-9982.

PDB codes: 2nzw 2nzx 2nzy

17009278 A.W.Truman, L.Robinson, and J.B.Spencer (2006).
Identification of a deacetylase involved in the maturation of teicoplanin.

Chembiochem, 7, 1670-1675.

16669774 D.Bowles, E.K.Lim, B.Poppenberger, and F.E.Vaistij (2006).
Glycosyltransferases of lipophilic small molecules.

Annu Rev Plant Biol, 57, 567-597.

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.

EMBO J, 25, 1396-1405.

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.

Mol Biosyst, 1, 117-126.

15926195 E.K.Lim (2005).
Plant glycosyltransferases: their potential as novel biocatalysts.

Chemistry, 11, 5486-5494.

15980457 P.Kamra, R.S.Gokhale, and D.Mohanty (2005).
SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites.

Nucleic Acids Res, 33, W220-W225.

16311633 T.Bililign, B.R.Griffith, and J.S.Thorson (2005).
Structure, activity, synthesis and biosynthesis of aryl-C-glycosides.

Nat Prod Rep, 22, 742-760.

15241472 E.K.Lim, and D.J.Bowles (2004).
A class of plant glycosyltransferases involved in cellular homeostasis.

EMBO J, 23, 2915-2922.

15028730 H.Korres, and N.K.Verma (2004).
Topological analysis of glucosyltransferase GtrV of Shigella flexneri by a dual reporter system and identification of a unique reentrant loop.

J Biol Chem, 279, 22469-22476.

15255862 J.Hans, W.Brandt, and T.Vogt (2004).
Site-directed mutagenesis and protein 3D-homology modelling suggest a catalytic mechanism for UDP-glucose-dependent betanidin 5-O-glucosyltransferase from Dorotheanthus bellidiformis.

Plant J, 39, 319-333.

15148316 M.L.Rosén, M.Edman, M.Sjöström, and A.Wieslander (2004).
Recognition of fold and sugar linkage for glycosyltransferases by multivariate sequence analysis.

J Biol Chem, 279, 38683-38692.

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

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.

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.

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.

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.

11752437 H.Chen, C.C.Tseng, B.K.Hubbard, and C.T.Walsh (2001).
Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine.

Proc Natl Acad Sci U S A, 98, 14901-14906.

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.