7D27 | pdb_00007d27

Structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase

• PDB DOI: https://doi.org/10.2210/pdb7D27/pdb

• Classification: LIGASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-16 Released: 2021-07-28 
• Deposition Author(s): Park, H.H., Jeong, K.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.229 (DCC) 

Starting Model: experimental

Literature

Wide-open conformation of UDP-MurNc-tripeptide ligase revealed by the substrate-free structure of MurE from Acinetobacter baumannii.

Jung, K.H., Kim, Y.G., Kim, C.M., Ha, H.J., Lee, C.S., Lee, J.H., Park, H.H.

(2021) FEBS Lett 595: 275-283

• PubMed: 33230844 
• DOI: https://doi.org/10.1002/1873-3468.14007
• Primary Citation Related Structures: 
  7D27


• PubMed Abstract: 
  

  MurE ligase catalyzes the attachment of meso-diaminopimelic acid to the UDP-MurNAc- _l -Ala- _d -Glu using ATP and producing UDP-MurNAc- _l -Ala- _d -Glu-meso-A ₂ pm during bacterial cell wall biosynthesis. Owing to the critical role of this enzyme, MurE is considered an attractive target for antibacterial drugs. Despite extensive studies on MurE ligase, the structural dynamics of its conformational changes are still elusive. In this study, we present the substrate-free structure of MurE from Acinetobacter baumannii, which is an antibiotic-resistant superbacterium that has threatened global public health. The structure revealed that MurE has a wide-open conformation and undergoes wide-open, intermediately closed, and fully closed dynamic conformational transition. Unveiling structural dynamics of MurE will help to understand the working mechanism of this ligase and to design next-generation antibiotics targeting MurE.

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Organizational Affiliation: 
• Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea.
College of Pharmacy, Chung-Ang University, Seoul, Korea.
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Korea.
College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, Korea.
Unit of Research for Practical Application, Korea Polar Research Institute, Incheon, Korea.
Department of Polar Sciences, University of Science and Technology, Incheon, Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 55.12 kDa 
• Atom Count: 3,932 
• Modeled Residue Count: 487 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase	A	499	Acinetobacter baumannii	Mutation(s): 0  Gene Names: murE, EA667_001595, EA685_00960, EA746_009110 EC: 6.3.2.13

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.229 (DCC) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.96	α = 90
b = 119.96	β = 90
c = 116.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxDC	data collection
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Park, H.H., Jeong, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description