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

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Basic information

Entry
Database: PDB / ID: 9dqf
TitleCrystal structure of bifunctional GlmU from Staphylococcus aureus NCTC 8325 complexed with acetyl CoA and citrate
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 wall organization / cell morphogenesis / 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 wall organization / cell morphogenesis / 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
ACETYL COENZYME *A / CITRIC ACID / Bifunctional protein GlmU
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 24, 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)50,7243
Polymers49,7231
Non-polymers1,0022
Water3,423190
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)152,1739
Polymers149,1683
Non-polymers3,0056
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)95.980, 95.980, 277.827
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-746-

HOH

21A-785-

HOH

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Components

#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)
Strain: NCTC 8325 / PS 47 / Gene: glmU, SAOUHSC_00471 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2G0S3, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.33 % / Description: Trapezoid morphology
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: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→46.3 Å / Num. obs: 39299 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.033 / Rrim(I) all: 0.149 / Χ2: 1 / Net I/σ(I): 13.6 / Num. measured all: 792650
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 100 % / Redundancy: 21 % / Rmerge(I) obs: 2.602 / Num. measured all: 52327 / Num. unique obs: 2491 / CC1/2: 0.68 / Rpim(I) all: 0.58 / Rrim(I) all: 2.666 / Χ2: 0.95 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.1 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1984 5.06 %
Rwork0.1983 --
obs0.2001 39214 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 64 190 3550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083422
X-RAY DIFFRACTIONf_angle_d0.9134662
X-RAY DIFFRACTIONf_dihedral_angle_d10.289499
X-RAY DIFFRACTIONf_chiral_restr0.063552
X-RAY DIFFRACTIONf_plane_restr0.011613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30541360.29062629X-RAY DIFFRACTION100
1.95-20.30411580.27072644X-RAY DIFFRACTION100
2-2.060.34651510.25442582X-RAY DIFFRACTION100
2.06-2.130.24341410.23572629X-RAY DIFFRACTION100
2.13-2.20.26351510.22182629X-RAY DIFFRACTION100
2.2-2.290.26091270.20782666X-RAY DIFFRACTION100
2.29-2.390.25541300.20222638X-RAY DIFFRACTION100
2.39-2.520.26481400.20412658X-RAY DIFFRACTION100
2.52-2.680.25411500.20472627X-RAY DIFFRACTION100
2.68-2.880.26831220.19862687X-RAY DIFFRACTION100
2.88-3.170.24671500.19512643X-RAY DIFFRACTION100
3.17-3.630.19961350.19552693X-RAY DIFFRACTION100
3.63-4.580.21411460.16742702X-RAY DIFFRACTION100
4.58-41.10.19211470.19132803X-RAY DIFFRACTION99

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