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- PDB-9sqg: PaMurU in complex with Mn2+ and UDPNAM (uridine diphosphate N-ace... -

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Basic information

Entry
Database: PDB / ID: 9sqg
TitlePaMurU in complex with Mn2+ and UDPNAM (uridine diphosphate N-acetyl muramic acid)
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
Chem-EPZ / : / PHOSPHATE ION / N-acetylmuramate alpha-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)80,98918
Polymers78,2353
Non-polymers2,75315
Water6,035335
1
C: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9035
Polymers26,0781
Non-polymers8254
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)26,9956
Polymers26,0781
Non-polymers9175
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)27,0907
Polymers26,0781
Non-polymers1,0126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.776, 51.779, 72.543
Angle α, β, γ (deg.)90.622, 90.674, 102.603
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
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 , 6 types, 350 molecules

#2: 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: obtained synthetically / Formula: C20H31N3O19P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 49.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES 0.1M pH=7.5, 0.2M NaCl 25% PEG335 / 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: Jun 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→72.53 Å / Num. obs: 60416 / % possible obs: 96.3 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3565 / CC1/2: 0.648 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→72.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.998 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2149 2936 4.86 %
Rwork0.1769 57475 -
all0.179 --
obs-60411 96.32 %
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: 32.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.126 Å2-0.151 Å22.595 Å2
2---0.181 Å21.844 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.85→72.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5128 0 158 335 5621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125405
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165032
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.8667355
X-RAY DIFFRACTIONr_angle_other_deg0.5541.77111569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.593548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5310811
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.38710246
X-RAY DIFFRACTIONr_chiral_restr0.0830.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
X-RAY DIFFRACTIONr_nbd_refined0.2120.21047
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24609
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22555
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2278
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.213
X-RAY DIFFRACTIONr_nbd_other0.1670.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.235
X-RAY DIFFRACTIONr_mcbond_it2.3852.9162684
X-RAY DIFFRACTIONr_mcbond_other2.3842.9162684
X-RAY DIFFRACTIONr_mcangle_it3.3615.2223348
X-RAY DIFFRACTIONr_mcangle_other3.3615.2223349
X-RAY DIFFRACTIONr_scbond_it3.5193.312721
X-RAY DIFFRACTIONr_scbond_other3.5183.3112722
X-RAY DIFFRACTIONr_scangle_it5.4385.8714007
X-RAY DIFFRACTIONr_scangle_other5.4375.8714008
X-RAY DIFFRACTIONr_lrange_it6.61832.5225839
X-RAY DIFFRACTIONr_lrange_other6.6131.295788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.281820.2824076X-RAY DIFFRACTION93.1117
1.898-1.950.2681740.2464175X-RAY DIFFRACTION95.8141
1.95-2.0060.2742540.2313969X-RAY DIFFRACTION95.8683
2.006-2.0680.2722060.2193915X-RAY DIFFRACTION96.0158
2.068-2.1360.2432170.2023801X-RAY DIFFRACTION97.1235
2.136-2.2110.221970.1873633X-RAY DIFFRACTION96.5222
2.211-2.2940.2371920.1773556X-RAY DIFFRACTION96.6727
2.294-2.3880.2511790.1653427X-RAY DIFFRACTION96.7534
2.388-2.4940.211610.173295X-RAY DIFFRACTION96.6443
2.494-2.6150.2541460.1743129X-RAY DIFFRACTION96.0411
2.615-2.7570.2241150.1742980X-RAY DIFFRACTION96.2974
2.757-2.9240.2391730.1782823X-RAY DIFFRACTION97.1781
2.924-3.1250.2351130.1732671X-RAY DIFFRACTION97.479
3.125-3.3750.1961280.1742498X-RAY DIFFRACTION96.8289
3.375-3.6960.2271160.1812313X-RAY DIFFRACTION96.9661
3.696-4.1310.1611160.1542026X-RAY DIFFRACTION97.7636
4.131-4.7680.201930.1491831X-RAY DIFFRACTION96.9269
4.768-5.8330.1731000.1591506X-RAY DIFFRACTION96.1677
5.833-8.2230.157440.1641193X-RAY DIFFRACTION96.8677
8.223-72.530.189300.169657X-RAY DIFFRACTION95.2843
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)
10.3515-0.0954-0.00060.45320.0090.315-0.0534-0.0001-0.02380.01760.04040.0202-0.00330.03420.0130.0123-0.001-0.00430.0259-0.00390.021115.709517.87483.8006
20.33020.0508-0.08780.4025-0.04050.50960.05180.02050.02160.0512-0.0157-0.00290.0033-0.0217-0.03620.02980.0109-0.00520.0096-0.00150.00625.4819-4.373126.3737
30.50950.10340.010.3885-0.12730.46220.0023-0.02740.0157-0.03340.0154-0.0189-0.0133-0.0457-0.01760.0229-0.0038-0.00690.0169-0.00440.0144-5.1019-16.4104-17.759
Refinement TLS groupSelection: ALL

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