2IV3 | pdb_00002iv3

Crystal structure of AviGT4, a glycosyltransferase involved in Avilamycin A biosynthesis

PDB DOI: https://doi.org/10.2210/pdb2IV3/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces viridochromogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-06-08 Released: 2006-10-11
Deposition Author(s): Martinez-Fleites, C., Proctor, M., Roberts, S., Bolam, D.N., Gilbert, H.J., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.273 (Depositor), 0.275 (DCC)
R-Value Work:
0.207 (Depositor), 0.211 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Insights Into the Synthesis of Lipopolysaccharide and Antibiotics Through the Structures of Two Retaining Glycosyltransferases from Family Gt4

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

(2006) Chem Biol 13: 1143

PubMed: 17113996 Search on PubMed
DOI: https://doi.org/10.1016/j.chembiol.2006.09.005
Primary Citation Related Structures:
2IUY, 2IV3, 2IV7, 2IW1

PubMed 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.

Organizational Affiliation

York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom.

Macromolecule Content

Total Structure Weight: 146.55 kDa
Atom Count: 10,607
Modeled Residue Count: 1,349
Deposited Residue Count: 1,368
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSYLTRANSFERASE	A, B, C, D	342	Streptomyces viridochromogenes	Mutation(s): 0
UniProt
Find proteins for Q93KV2 (Streptomyces viridochromogenes Tue57) Explore Q93KV2 Go to UniProtKB: Q93KV2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93KV2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.273 (Depositor), 0.275 (DCC)
R-Value Work: 0.207 (Depositor), 0.211 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.47	α = 89.99
b = 74.37	β = 92.7
c = 90.64	γ = 100.73

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-10-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-10-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description