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- PDB-9sqe: PaMurU in complex with Mg2+ cofactor and UDPNAM/Diphosphate products -

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Basic information

Entry
Database: PDB / ID: 9sqe
TitlePaMurU in complex with Mg2+ cofactor and UDPNAM/Diphosphate products
ComponentsN-acetylmuramate alpha-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / Pseudonomas aeruginosa Peptidoglycan recycling pathway Bacteria cell wall
Function / homology
Function and homology information


N-acetyl-alpha-D-muramate 1-phosphate uridylyltransferase / peptidoglycan turnover / peptidoglycan biosynthetic process / nucleotidyltransferase activity / cell wall organization / regulation of cell shape / response to antibiotic / metal ion binding
Similarity search - Function
: / : / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
DIPHOSPHATE / Chem-EPZ / DI(HYDROXYETHYL)ETHER / N-acetylmuramate alpha-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJimenez-Faraco, E. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2023-153118OB-I00 Spain
CitationJournal: Acs Catalysis / Year: 2026
Title: Catalytic Cycle of N-Acetylmuramic Acid-alpha-1-Phosphate Uridylyltransferase MurU of Pseudomonas aeruginosa
Authors: Jimenez-Faraco, E. / El-Araby, A.M. / Feltzer, R. / Nguyen, V.T. / Mobashery, S. / Hermoso, J.A.
History
DepositionSep 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: N-acetylmuramate alpha-1-phosphate uridylyltransferase
A: N-acetylmuramate alpha-1-phosphate uridylyltransferase
B: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,25918
Polymers78,2353
Non-polymers3,02415
Water7,350408
1
C: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0866
Polymers26,0781
Non-polymers1,0085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0866
Polymers26,0781
Non-polymers1,0085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0866
Polymers26,0781
Non-polymers1,0085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.706, 51.719, 72.834
Angle α, β, γ (deg.)90.535, 90.539, 102.568
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 3 molecules CAB

#1: Protein N-acetylmuramate alpha-1-phosphate uridylyltransferase / MurNAc-1P uridylyltransferase / MurNAc-alpha-1P uridylyltransferase


Mass: 26078.389 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Molecule 3 is the same that the others. The entry code in uniprot is Q9I5U0
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: murU, PA0597 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I5U0, N-acetyl-alpha-D-muramate 1-phosphate uridylyltransferase

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Non-polymers , 5 types, 423 molecules

#2: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPZ / (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid


Mass: 679.416 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C20H31N3O19P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES 0.1M pH=7.5, 0.2M NaCl 25% PEG3350 / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.1→51.94 Å / Num. obs: 40882 / % possible obs: 93.8 % / Redundancy: 3.5 % / CC1/2: 0.978 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 3225 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDS1.2data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.749 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.96 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.246 / ESU R Free: 0.189
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.205 1794 4.95 %
Rwork0.1555 34447 -
all0.158 --
obs-36241 96.88 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.321 Å2
Baniso -1Baniso -2Baniso -3
1--0.004 Å2-0.165 Å21.052 Å2
2--0.134 Å21.229 Å2
3----0.132 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5105 0 186 408 5699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125409
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165033
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.8667360
X-RAY DIFFRACTIONr_angle_other_deg0.5251.77111569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.777548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05210808
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.91110245
X-RAY DIFFRACTIONr_chiral_restr0.0770.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021218
X-RAY DIFFRACTIONr_nbd_refined0.220.21073
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.24588
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22533
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2328
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0750.217
X-RAY DIFFRACTIONr_nbd_other0.160.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.234
X-RAY DIFFRACTIONr_mcbond_it1.4461.6442667
X-RAY DIFFRACTIONr_mcbond_other1.4461.6442667
X-RAY DIFFRACTIONr_mcangle_it2.3292.943325
X-RAY DIFFRACTIONr_mcangle_other2.3282.9413326
X-RAY DIFFRACTIONr_scbond_it2.1581.932742
X-RAY DIFFRACTIONr_scbond_other2.1571.932743
X-RAY DIFFRACTIONr_scangle_it3.5393.414035
X-RAY DIFFRACTIONr_scangle_other3.5393.4114036
X-RAY DIFFRACTIONr_lrange_it4.91518.165908
X-RAY DIFFRACTIONr_lrange_other4.87217.6625819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.2631240.17124500.17527780.9580.98292.65660.166
2.257-2.3190.2331200.16724600.1726740.9710.98396.48470.163
2.319-2.3860.2171700.15123860.15526260.9720.98797.33440.15
2.386-2.4590.2381090.14624130.1525840.9680.98797.60060.147
2.459-2.5390.2491300.15822230.16324170.9630.98597.35210.161
2.539-2.6280.2211240.15322050.15723900.9720.98697.44770.157
2.628-2.7270.2151180.15221290.15523100.9720.98697.27270.159
2.727-2.8380.195830.14620600.14721900.9720.98797.85390.154
2.838-2.9630.2021120.15419560.15721260.9760.98597.27190.167
2.963-3.1070.224900.16319020.16620450.9680.98597.40830.176
3.107-3.2740.2451130.1717320.17519050.9630.98496.85040.188
3.274-3.4710.223700.1817390.18118580.9730.98497.36280.202
3.471-3.7090.208560.17316230.17417200.9720.98597.61630.191
3.709-4.0040.177950.14314520.14515930.9820.98997.11240.166
4.004-4.3820.158530.12713640.12814690.9890.99196.46020.157
4.382-4.8920.18510.13212150.13413100.9840.99196.64120.159
4.892-5.6360.14580.14711000.14711840.9910.99197.80410.184
5.636-6.8720.206400.189270.1819940.9770.98697.28370.217
6.872-9.5890.16570.136970.1327790.9880.99196.79080.171
9.589-41.7490.189210.1914140.1914530.9830.97896.02650.301
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3858-0.06360.00530.3524-0.0230.26790.05690.02350.01740.0236-0.0708-0.02260.03290.00260.01390.0233-0.0031-0.00030.01450.00380.0124-15.1243-18.4642-3.5826
20.23750.0806-0.1630.4029-0.02780.54810.0346-0.0313-0.0121-0.0193-0.02280.011-0.0325-0.007-0.01180.0205-0.0086-0.00410.0163-0.0010.0045-26.5093-41.070218.0758
30.43390.02230.01480.3323-0.04720.4966-0.04390.0265-0.02370.01280.06470.0306-0.0180.0051-0.02080.00830.00780.00630.03720.010.0062-36.2397-53.8666-26.2712
Refinement TLS groupSelection: ALL

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