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2dln, resolution 2.30Å ()
Ligands: , ,
Activity: D-alanine--D-alanine ligase, with EC number
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Publication Abstract from PubMed

The molecular structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli, co-crystallized with an S,R-methylphosphinate and adenosine triphosphate, was determined by x-ray diffraction to a resolution of 2.3 angstroms. A catalytic mechanism for the ligation of two D-alanine substrates is proposed in which a helix dipole and a hydrogen-bonded triad of tyrosine, serine, and glutamic acid assist binding and deprotonation steps. From sequence comparison, it is proposed that a different triad exists in a recently discovered D-alanine:D-lactate ligase (VanA) present in vancomycin-resistant enterococci. A molecular mechanism for the altered specificity of VanA is suggested.

Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution., Fan C, Moews PC, Walsh CT, Knox JR, Science. 1994 Oct 21;266(5184):439-43. PMID:7939684

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

2dln is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA.


  • Fan C, Moews PC, Walsh CT, Knox JR. Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution. Science. 1994 Oct 21;266(5184):439-43. PMID:7939684
  • Fan C, Park IS, Walsh CT, Knox JR. D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Biochemistry. 1997 Mar 4;36(9):2531-8. PMID:9054558 doi:10.1021/bi962431t
  • Lee JH, Na Y, Song HE, Kim D, Park BH, Rho SH, Im YJ, Kim MK, Kang GB, Lee DS, Eom SH. Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes. Proteins. 2006 Sep 1;64(4):1078-82. PMID:16779845 doi:http://dx.doi.org/10.1002/prot.20927

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