4C5A

The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and D-cycloserine phosphate

• PDB DOI: https://doi.org/10.2210/pdb4C5A/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12, synthetic construct
• 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: 1.65 Å
• R-Value Free: 0.237 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

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: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content

• Total Structure Weight: 74.12 kDa 
• Atom Count: 5,100 
• Modelled Residue Count: 618 
• Deposited Residue Count: 668 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE	C	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], J [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
DS0	E [auth A], K [auth B]	[(4R)-4-azanyl-4,5-dihydro-1,2-oxazol-3-yl] dihydrogen phosphate C3 H7 N2 O5 P SFMNESRSKJTEMJ-UWTATZPHSA-N
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A], G [auth A], L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.237 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.79	α = 90
b = 97.51	β = 90
c = 109.99	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, Source and taxonomy
• Version 1.2: 2019-10-09
  Changes: Data collection, Other, Source and taxonomy
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description