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2dln

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2dln, resolution 2.30Å ()

Ligands:

, ,

Activity:

D-alanine--D-alanine ligase, with EC number 6.3.2.4

Structural annotation:
Resources:	CATH : 2Dln002, 2Dln001, 2Dln003 InterPro : Ipr011761, Ipr005905, Ipr000291, Ipr011095, Ipr013816, Ipr013817, Ipr011127 Pfam : PF07478, PF01820 SCOP : d2dln_2, d2dln_1 UniProt : P07862

Functional annotation:
Cellular component:	cell wall cytoplasm
Biological process:	cell wall organization and biogenesis peptidoglycan biosynthetic process regulation of cell shape
Molecular function:	catalytic activity D-alanine-D-alanine ligase activity ligase activity ATP binding

Evolutionary conservation:

Toggle Conservation Colors:	Rows = identical sequences:
Further Information:	Caveats, Explanation, Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, RCSB, PDBsum

Coordinates:

save as pdb, mmCIF, xml

VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTION

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.

Reference

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:10.1002/prot.20927