4C5B

The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ATP and D-ala-D-ala

• PDB DOI: https://doi.org/10.2210/pdb4C5B/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-10 Released: 2015-01-21 
• Deposition Author(s): Batson, S., Majce, V., Lloyd, A.J., Rea, D., Fishwick, C.W.G., Simmons, K.J., Fulop, V., Roper, D.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.

Batson, S., de Chiara, C., Majce, V., Lloyd, A.J., Gobec, S., Rea, D., Fulop, V., Thoroughgood, C.W., Simmons, K.J., Dowson, C.G., Fishwick, C.W.G., de Carvalho, L.P.S., Roper, D.I.

(2017) Nat Commun 8: 1939-1939

• PubMed: 29208891 
• DOI: https://doi.org/10.1038/s41467-017-02118-7
• Primary Citation of Related Structures:  
  4C5A, 4C5B, 4C5C


• PubMed Abstract: 
  

  D-cycloserine is an antibiotic which targets sequential bacterial cell wall peptidoglycan biosynthesis enzymes: alanine racemase and D-alanine:D-alanine ligase. By a combination of structural, chemical and mechanistic studies here we show that the inhibition of D-alanine:D-alanine ligase by the antibiotic D-cycloserine proceeds via a distinct phosphorylated form of the drug. This mechanistic insight reveals a bimodal mechanism of action for a single antibiotic on different enzyme targets and has significance for the design of future inhibitor molecules based on this chemical structure.

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Organizational Affiliation: 

School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.41 kDa 
• Atom Count: 5,483 
• Modelled Residue Count: 612 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ALANINE--D-ALANINE LIGASE	A, B	330	Escherichia coli K-12	Mutation(s): 0  EC: 6.3.2.4
UniProt
Find proteins for P07862 (Escherichia coli (strain K12)) Explore P07862  Go to UniProtKB:  P07862

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], L [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DAL	D [auth A], E [auth A], M [auth B], N [auth B]	D-ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-UWTATZPHSA-N
IMD	K [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CO3	F [auth A], O [auth B]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
MG	G [auth A], H [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53	α = 90
b = 97.62	β = 90
c = 109.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Batson, S., Majce, V., Lloyd, A.J., Rea, D., Fishwick, C.W.G., Simmons, K.J., Fulop, V., Roper, D.I.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description