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- EMDB-80332: Peptidoglycan and lipopolysaccharide biosynthesis enzymes with in... -

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Basic information

Entry
Database: EMDB / ID: EMD-80332
TitlePeptidoglycan and lipopolysaccharide biosynthesis enzymes with inhibitor
Map data
Sample
  • Complex: PaMurA-PaLpxC complex in the presence of CHIR-090
    • Protein or peptide: UDP-N-acetylglucosamine 1-carboxyvinyltransferase,UDP-3-O-acyl-N-acetylglucosamine deacetylase
  • Ligand: N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide
Keywordsbiogenesis / peptidoglycan synthesis enzyme / lipopolysaccharide synthesis enzyme / bacterial cell wall / bacterial outer membrane / BIOSYNTHETIC PROTEIN
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
UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsYeo JY / Yan XF / Gao YG
Funding support Singapore, 1 items
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, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_80332.png

Downloads & links

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Map

FileDownload / File: emd_80332.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 256 pix.
= 194.56 Å		0.76 Å/pix.
x 256 pix.
= 194.56 Å		0.76 Å/pix.
x 256 pix.
= 194.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.07224247 - 0.1793308
Average (Standard dev.)-0.00013776048 (±0.00474174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 194.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_80332_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80332_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : PaMurA-PaLpxC complex in the presence of CHIR-090

EntireName: PaMurA-PaLpxC complex in the presence of CHIR-090
Components
  • Complex: PaMurA-PaLpxC complex in the presence of CHIR-090
    • Protein or peptide: UDP-N-acetylglucosamine 1-carboxyvinyltransferase,UDP-3-O-acyl-N-acetylglucosamine deacetylase
  • Ligand: N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide

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Supramolecule #1: PaMurA-PaLpxC complex in the presence of CHIR-090

SupramoleculeName: PaMurA-PaLpxC complex in the presence of CHIR-090 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 78.06 kDa/nm

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Macromolecule #1: UDP-N-acetylglucosamine 1-carboxyvinyltransferase,UDP-3-O-acyl-N-...

MacromoleculeName: UDP-N-acetylglucosamine 1-carboxyvinyltransferase,UDP-3-O-acyl-N-acetylglucosamine deacetylase
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 78.149594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDKLIITGGN RLDGEIRISG AKNSALPILA ATLLADTPVT VCNLPHLHDI TTMIELFGRM GVQPIIDEKL NVEVDASSIK TLVAPYELV KTMRASILVL GPMLARFGEA EVALPGGCAI GSRPVDLHIR GLEAMGAQIE VEGGYIKAKA PAGGLRGGHF F FDTVSVTG ...String:
MDKLIITGGN RLDGEIRISG AKNSALPILA ATLLADTPVT VCNLPHLHDI TTMIELFGRM GVQPIIDEKL NVEVDASSIK TLVAPYELV KTMRASILVL GPMLARFGEA EVALPGGCAI GSRPVDLHIR GLEAMGAQIE VEGGYIKAKA PAGGLRGGHF F FDTVSVTG TENLMMAAAL ANGRTVLQNA AREPEVVDLA NCLNAMGANV QGAGSDTIVI EGVKRLGGAR YDVLPDRIET GT YLVAAAA TGGRVKLKDT DPTILEAVLQ KLEEAGAHIS TGSNWIELDM KGNRPKAVNV RTAPYPAFPT DMQAQFISMN AVA EGTGAV IETVFENRFM HVYEMNRMGA QILVEGNTAI VTGVPKLKGA PVMATDLRAS ASLVIAGLVA EGDTLIDRIY HIDR GYECI EEKLQLLGAK IRRVPGMIKQ RTLKNIIRAT GVGLHSGEKV YLTLKPAPVD TGIVFCRTDL DPVVEIPARA ENVGE TTMS TTLVKGDVKV DTVEHLLSAM AGLGIDNAYV ELSASEVPIM DGSAGPFVFL IQSAGLQEQE AAKKFIRIKR EVSVEE GDK RAVFVPFDGF KVSFEIDFDH PVFRGRTQQA SVDFSSTSFV KEVSRARTFG FMRDIEYLRS QNLALGGSVE NAIVVDE NR VLNEDGLRYE DEFVKHKILD AIGDLYLLGN SLIGEFRGFK SGHALNNQLL RTLIADKDAW EVVTFEDART APISYMRP A AAV

UniProtKB: UDP-N-acetylglucosamine 1-carboxyvinyltransferase, UDP-3-O-acyl-N-acetylglucosamine deacetylase

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Macromolecule #2: N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(mor...

MacromoleculeName: N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide
type: ligand / ID: 2 / Number of copies: 1 / Formula: C90
Molecular weightTheoretical: 437.488 Da
Chemical component information

ChemComp-C90:
N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
20.0 mMTris
150.0 mMSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5bq2


Details: 5U39
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 275131
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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