4C5C | pdb_00004c5c

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

• PDB DOI: https://doi.org/10.2210/pdb4C5C/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: 1.40 Å
• R-Value Free: 
  0.203 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

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 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.
Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.
Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, NW1 1AT, London, UK. [e-mail].
School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK. [e-mail].

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: 5,365 
• Modeled 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A], K [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DAL	D [auth A], E [auth A], L [auth B], M [auth B]	D-ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-UWTATZPHSA-N
MG	F [auth A], G [auth A], H [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.203 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.23	α = 90
b = 97.8	β = 90
c = 110.12	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