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- PDB-25rw: Peptidoglycan and lipopolysaccharide biosynthesis enzymes with in... -

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Basic information

Entry
Database: PDB / ID: 25rw
TitlePeptidoglycan and lipopolysaccharide biosynthesis enzymes with inhibitor
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase,UDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsBIOSYNTHETIC PROTEIN / biogenesis / peptidoglycan synthesis enzyme / lipopolysaccharide synthesis enzyme / bacterial cell wall / bacterial outer membrane
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm
Similarity search - Function
: / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-C90 / UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsYeo, J.Y. / Yan, X.F. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: J Struct Biol / Year: 2026
Title: Structure of the MurA-LpxC enzyme complex in modulating peptidoglycan and lipopolysaccharide biosynthesis.
Authors: Joshua Yi Yeo / Xin-Fu Yan / Zhu Qiao / Yan Yu Liew / Phong Hoa Do / Yuguang Mu / Yong-Gui Gao /
Abstract: Coordination of peptidoglycan and lipopolysaccharide biosynthesis is essential for maintaining Gram-negative cell envelope homeostasis. Two enzymes, MurA and LpxC, catalyze the first committed steps ...Coordination of peptidoglycan and lipopolysaccharide biosynthesis is essential for maintaining Gram-negative cell envelope homeostasis. Two enzymes, MurA and LpxC, catalyze the first committed steps in peptidoglycan and lipopolysaccharide biosynthesis, respectively. Here, we determined cryo-electron microscopy (cryo-EM) structures of the Pseudomonas aeruginosa MurA-LpxC complex in the absence and presence of the LpxC inhibitor CHIR-090, providing molecular insights into complex formation. Structure-guided mutagenesis of MurA, together with in vitro pull-down assays, identified residues crucial for complex formation. We show that MurA G58 favors, but is not sufficient for complex formation, as substitution of this residue to mimic Escherichia coli MurA (G58S) weakens the interaction. Together, our study advances our structural understanding of how two biosynthesis pathways for peptidoglycan and lipopolysaccharide are coordinated to maintain a synergistic and balanced cell envelope.
History
DepositionApr 16, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase,UDP-3-O-acyl-N-acetylglucosamine deacetylase
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase,UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,7373
Polymers156,2992
Non-polymers4371
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein UDP-N-acetylglucosamine 1-carboxyvinyltransferase,UDP-3-O-acyl-N-acetylglucosamine deacetylase / Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT / UDP-3-O-acyl- ...Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT / UDP-3-O-acyl-GlcNAc deacetylase / UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase


Mass: 78149.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: murA, PA4450, lpxC, envA, PA4406 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HVW7, UniProt: P47205, UDP-N-acetylglucosamine 1-carboxyvinyltransferase, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-C90 / N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide


Mass: 437.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N3O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PaMurA-PaLpxC complex in the presence of CHIR-090 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 78.06 kDa/nm / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMTris1
2150 mMSodium Chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275131 / Symmetry type: POINT
RefinementCross valid method: NONE

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