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- PDB-9dr4: Crystal structure of bifunctional GlmU from Staphylococcus aureus... -

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Basic information

Entry
Database: PDB / ID: 9dr4
TitleCrystal structure of bifunctional GlmU from Staphylococcus aureus NCTC 8325 complexed with UTP, CoA and Glc 1-P
ComponentsBifunctional protein GlmU
KeywordsTRANSFERASE / uridyltransferase / acetyltransferase
Function / homology
Function and homology information


glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape / magnesium ion binding / membrane / cytoplasm
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
COENZYME A / 1-O-phosphono-alpha-D-glucopyranose / URIDINE 5'-TRIPHOSPHATE / Bifunctional protein GlmU
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPederick, J.L. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2025
Title: Functional and structural characterization of Staphylococcus aureus N-acetylglucosamine 1-phosphate uridyltransferase (GlmU) reveals a redox-sensitive acetyltransferase activity.
Authors: Pederick, J.L. / Kumar, A. / Pukala, T.L. / Bruning, J.B.
History
DepositionSep 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2595
Polymers49,7231
Non-polymers1,5364
Water4,720262
1
A: Bifunctional protein GlmU
hetero molecules

A: Bifunctional protein GlmU
hetero molecules

A: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,77715
Polymers149,1683
Non-polymers4,60812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area18940 Å2
ΔGint-60 kcal/mol
Surface area48430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.883, 94.883, 262.532
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-216-

ARG

21A-502-

MG

31A-612-

HOH

41A-824-

HOH

51A-830-

HOH

61A-849-

HOH

71A-853-

HOH

81A-854-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Bifunctional protein GlmU


Mass: 49722.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: glmU, SAOUHSC_00471 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2G0S3, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#4: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 265 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.22 % / Description: Trapezoid
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium citrate tribasic tetrahydrate, 15 - 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→39.21 Å / Num. obs: 39284 / % possible obs: 100 % / Redundancy: 20.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.054 / Rrim(I) all: 0.245 / Χ2: 0.99 / Net I/σ(I): 12.1 / Num. measured all: 796494
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 100 % / Redundancy: 20.4 % / Rmerge(I) obs: 3.603 / Num. measured all: 49237 / Num. unique obs: 2410 / CC1/2: 0.526 / Rpim(I) all: 0.814 / Rrim(I) all: 3.695 / Χ2: 0.95 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.15data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.21 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 1996 5.09 %
Rwork0.1748 --
obs0.1767 39244 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 92 262 3673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093489
X-RAY DIFFRACTIONf_angle_d1.0244764
X-RAY DIFFRACTIONf_dihedral_angle_d14.131232
X-RAY DIFFRACTIONf_chiral_restr0.068568
X-RAY DIFFRACTIONf_plane_restr0.009616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.32741400.28752628X-RAY DIFFRACTION100
1.9-1.950.27571610.25472623X-RAY DIFFRACTION100
1.95-20.29081430.22832607X-RAY DIFFRACTION100
2-2.070.26891470.20982643X-RAY DIFFRACTION100
2.07-2.140.23061550.19322611X-RAY DIFFRACTION100
2.14-2.230.241270.17992661X-RAY DIFFRACTION100
2.23-2.330.22211170.17292656X-RAY DIFFRACTION100
2.33-2.450.22771520.16962644X-RAY DIFFRACTION100
2.45-2.610.23641470.17482623X-RAY DIFFRACTION100
2.61-2.810.2291260.17352697X-RAY DIFFRACTION100
2.81-3.090.19681520.17112639X-RAY DIFFRACTION100
3.09-3.540.22381290.16652700X-RAY DIFFRACTION100
3.54-4.460.16061500.14442710X-RAY DIFFRACTION100
4.46-39.210.18791500.16452806X-RAY DIFFRACTION99

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