PDB-9sqd: PaMurU in complex with their natural substrates (UTP and NAM-1P) ...

ID or keywords:

Entry

Database: PDB / ID: 9sqd

Title

PaMurU in complex with their natural substrates (UTP and NAM-1P) and Mg2+ cofactor

Components

N-acetylmuramate alpha-1-phosphate uridylyltransferase

Keywords

TRANSFERASE / 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

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.951 Å

Authors

Jimenez-Faraco, E. / Hermoso, J.A.

Funding support

Spain, 1items

Citation

Journal: 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

Deposition	Sep 22, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9sqd.cif.gz	355 KB	Display	PDBx/mmCIF format
PDB format	pdb9sqd.ent.gz	218.1 KB	Display	PDB format
PDBx/mmJSON format	9sqd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sq/9sqd ftp://data.pdbj.org/pub/pdb/validation_reports/sq/9sqd	HTTPS FTP

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Related structure data

Related structure data	9smvC 9sqeC 9sqfC 9sqgC 9szkC 9szlC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

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

81 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: N-acetylmuramate alpha-1-phosphate uridylyltransferase

hetero molecules

defined by author
Evidence: equilibrium centrifugation, ultracentrifugation (SV-AUC)
27 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: N-acetylmuramate alpha-1-phosphate uridylyltransferase

hetero molecules

defined by author
27 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: N-acetylmuramate alpha-1-phosphate uridylyltransferase

hetero molecules

defined by author
27 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.567, 51.586, 72.725
Angle α, β, γ (deg.)	90.630, 90.531, 102.618
Int Tables number	1
Space group name H-M	P1

#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
#2: Sugar	ChemComp-491 / 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / N-acetyl-3-O-[(1R)-1-carboxyethyl]-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-glucose Type: D-saccharide / Mass: 373.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₁H₂₀NO₁₁P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE Mass: 484.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₅N₂O₁₅P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49.02 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 17, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 1.95→72.72 Å / Num. obs: 45729 / % possible obs: 85.9 % / Redundancy: 3.6 % / CC_1/2: 0.992 / R_merge(I) obs: 0.112 / Net I/σ(I): 7.4
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.587 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3531 / CC_1/2: 0.819 / % possible all: 94.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
autoPROC		data reduction
Aimless	0.7.15	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.951→72.715 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.91 / SU B: 10.236 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.232 / ESU R Free: 0.198
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2662	2392	5.231 %
R_work	0.22	43333	-
all	0.222	-	-
obs	-	45725	85.873 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 24.637 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.247 Å²	-0.346 Å²	1.391 Å²
2-	-	0.765 Å²	1.208 Å²
3-	-	-	-0.514 Å²

Refinement step

Cycle: LAST / Resolution: 1.951→72.715 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5106	0	165	204	5475

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	5392
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5005
X-RAY DIFFRACTION	r_angle_refined_deg	1.669	1.85	7346
X-RAY DIFFRACTION	r_angle_other_deg	0.561	1.764	11505
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.053	5	663
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.224	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.735	10	809
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.432	10	245
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	802
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6419
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1215
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1140
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	4619
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	2507
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2735
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	241
X-RAY DIFFRACTION	r_metal_ion_refined	0.076	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.116	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.144	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.589	2.071	2667
X-RAY DIFFRACTION	r_mcbond_other	1.589	2.071	2667
X-RAY DIFFRACTION	r_mcangle_it	2.452	3.71	3325
X-RAY DIFFRACTION	r_mcangle_other	2.453	3.711	3326
X-RAY DIFFRACTION	r_scbond_it	2.127	2.358	2725
X-RAY DIFFRACTION	r_scbond_other	2.119	2.357	2722
X-RAY DIFFRACTION	r_scangle_it	3.396	4.214	4021
X-RAY DIFFRACTION	r_scangle_other	3.389	4.212	4019
X-RAY DIFFRACTION	r_lrange_it	4.593	21.47	5868
X-RAY DIFFRACTION	r_lrange_other	4.578	21.278	5837

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.951-2.002	0.346	201	0.276	3477	0.28	3924	0.921	0.952	93.7309	0.261
2.002-2.057	0.317	186	0.26	3472	0.263	3864	0.936	0.958	94.6687	0.244
2.057-2.116	0.316	130	0.26	2522	0.262	3702	0.936	0.958	71.6369	0.242
2.116-2.181	0.3	180	0.249	3244	0.252	3632	0.945	0.962	94.2731	0.232
2.181-2.253	0.296	200	0.234	2500	0.238	3530	0.946	0.967	76.4873	0.217
2.253-2.332	0.296	163	0.227	2983	0.231	3405	0.949	0.969	92.3935	0.211
2.332-2.42	0.316	178	0.228	2888	0.233	3278	0.938	0.968	93.5326	0.213
2.42-2.518	0.278	136	0.234	2759	0.237	3137	0.951	0.967	92.2856	0.221
2.518-2.63	0.314	159	0.238	2610	0.242	3022	0.944	0.966	91.6281	0.227
2.63-2.758	0.258	113	0.213	1710	0.216	2898	0.954	0.973	62.9055	0.204
2.758-2.907	0.279	126	0.225	2327	0.227	2764	0.949	0.969	88.7482	0.219
2.907-3.083	0.267	92	0.23	2110	0.231	2608	0.954	0.968	84.4325	0.225
3.083-3.296	0.299	86	0.233	1700	0.236	2439	0.946	0.965	73.2267	0.23
3.296-3.559	0.251	91	0.242	1488	0.242	2251	0.965	0.968	70.1466	0.241
3.559-3.898	0.238	87	0.217	1362	0.219	2101	0.969	0.973	68.9672	0.214
3.898-4.356	0.182	61	0.175	1720	0.176	1910	0.983	0.982	93.2461	0.183
4.356-5.027	0.179	46	0.163	1588	0.163	1668	0.98	0.984	97.9616	0.174
5.027-6.15	0.226	63	0.197	1308	0.198	1403	0.984	0.98	97.7192	0.215
6.15-8.666	0.205	70	0.201	1007	0.201	1100	0.98	0.976	97.9091	0.221
8.666-72.715	0.26	24	0.218	558	0.22	606	0.962	0.967	96.0396	0.227

Refinement TLS params.

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

ID	L11 (°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)
1	0.3829	-0.0106	-0.0833	0.4066	-0.0872	0.1974	0.0351	0.0094	0.015	0.0182	-0.0661	-0.024	0.0349	0.0018	0.031	0.0451	0.0029	0.0171	0.0151	0.0014	0.02	-15.5498	-18.1326	-3.162
2	0.3575	0.0792	-0.1966	0.4415	-0.1363	0.5803	0.0422	-0.0477	-0.0236	-0.0375	-0.0288	0.0096	-0.0249	0.0008	-0.0134	0.05	-0.0128	0.0068	0.0144	-0.0002	0.0069	-26.7658	-40.73	18.4365
3	0.398	-0.0339	0.0396	0.2611	-0.0516	0.5737	-0.0344	0.0416	-0.0043	0.0283	0.0542	0.0334	0.0011	0.0107	-0.0198	0.0142	0.0084	0.0149	0.0386	0.0209	0.0222	-36.4498	-53.6254	-25.7439

Refinement TLS group

Selection: ALL

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