1GG4 | pdb_00001gg4

CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1GG4/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2000-07-12 Released: 2000-12-20 
• Deposition Author(s): Yan, Y., Munshi, S., Chen, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.280 (Depositor) 
• R-Value Work: 
  0.203 (Depositor) 

Literature

Crystal structure of Escherichia coli UDPMurNAc-tripeptide d-alanyl-d-alanine-adding enzyme (MurF) at 2.3 A resolution.

Yan, Y., Munshi, S., Leiting, B., Anderson, M.S., Chrzas, J., Chen, Z.

(2000) J Mol Biology 304: 435-445

• PubMed: 11090285 
• DOI: https://doi.org/10.1006/jmbi.2000.4215
• Primary Citation Related Structures: 
  1GG4


• PubMed Abstract: 
  

  MurF is required to catalyze the final step in the synthesis of the cytoplasmic precursor of the bacterial cell wall peptidoglycan, rendering it an attractive target for antibacterial drug development. The crystal structure of the MurF apo-enzyme has been determined using the multiwavelength anomalous dispersion method and refined to 2.3 A resolution. It contains three consecutive open alpha/beta-sheet domains. In comparison with the complex crystal structures of MurD and its substrates, The topology of the N-terminal domain of MurF is unique, while its central and C-terminal domains exhibit similar mononucleotide and dinucleotide-binding folds, respectively. The apo-enzyme of MurF crystal structure reveals an open conformation with the three domains juxtaposed in a crescent-like arrangement creating a wide-open space where substrates are expected to bind. As such, catalysis is not feasible and significant domain closure is expected upon substrate binding.

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Organizational Affiliation: 
• Department of Structural Biology, West Point, PA, 19486, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 95.82 kDa 
• Atom Count: 6,791 
• Modeled Residue Count: 878 
• Deposited Residue Count: 904 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE	A, B	452	Escherichia coli	Mutation(s): 9  EC: 6.3.2.15 (PDB Primary Data), 6.3.2.10 (UniProt)
UniProt
Find proteins for P11880 (Escherichia coli (strain K12)) Explore P11880  Go to UniProtKB:  P11880

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.280 (Depositor) 
• R-Value Work:  0.203 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.2	α = 90
b = 74.2	β = 90
c = 429.3	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
MLPHARE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-20 
Deposition Author(s): Yan, Y., Munshi, S., Chen, Z.

Revision History  

• Version 1.0: 2000-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-07-21
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references
• Version 1.6: 2024-10-09
  Changes: Structure summary