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- PDB-1uae: STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1uae
TitleSTRUCTURE OF UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
ComponentsUDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
KeywordsTRANSFERASE / PEPTIDOGLYCAN / UDP-N-ACETYLGLUCOSAMINE / FOSFOMYCIN
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytosol
Similarity search - Function
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / : / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
[(1R)-1-hydroxypropyl]phosphonic acid / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSkarzynski, T.
Citation
Journal: Structure / Year: 1996
Title: Structure of UDP-N-acetylglucosamine enolpyruvyl transferase, an enzyme essential for the synthesis of bacterial peptidoglycan, complexed with substrate UDP-N-acetylglucosamine and the drug fosfomycin.
Authors: Skarzynski, T. / Mistry, A. / Wonacott, A. / Hutchinson, S.E. / Kelly, V.A. / Duncan, K.
#1: Journal: J.Bacteriol. / Year: 1992
Title: Cloning and Sequencing of Escherichia Coli Murz and Purification of its Product, a Udp-N-Acetylglucosamine Enolpyruvyl Transferase
Authors: Marquardt, J.L. / Siegele, D.A. / Kolter, R. / Walsh, C.T.
History
DepositionSep 30, 1996Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2011Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6193
Polymers44,8721
Non-polymers7472
Water7,602422
1
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8579
Polymers134,6153
Non-polymers2,2426
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)110.660, 110.660, 67.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE / MURA


Mass: 44871.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P0A749, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Chemical ChemComp-FFQ / [(1R)-1-hydroxypropyl]phosphonic acid / Fosfomycin, bound form


Mass: 140.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 55 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22.5 mMUDP-GlcNAc1drop
325 %tert-butanol1reservoir
4100 mM1reservoirCaCl2
510 %glycerol1reservoir
6100 mMTris-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 9, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 41471 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 1.8 Å / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.185 -
obs0.185 40374
Displacement parametersBiso mean: 21.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 47 422 3602
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg2.85

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