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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1ehi
Jmol
Contents
Protein chains
360 a.a. *
Ligands
ADP
PHY
Metals
_MG ×2
Waters ×213
* Residue conservation analysis
PDB id:
1ehi
Name: Ligase
Title: D-alanine:d-lactate ligase (lmddl2) of vancomycin-resistant leuconostoc mesenteroides
Structure: D-alanine:d-lactate ligase. Chain: a, b. Synonym: lmddl2. Engineered: yes
Source: Leuconostoc mesenteroides. Organism_taxid: 1245. Atcc: 8293. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.38Å     R-factor:   0.184     R-free:   0.257
Authors: A.P.Kuzin,T.Sun,J.Jorczak-Baillass,V.L.Healy,C.T.Walsh, J.R.Knox
Key ref:
A.P.Kuzin et al. (2000). Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides. Structure, 8, 463-470. PubMed id: 10801495 DOI: 10.1016/S0969-2126(00)00129-5
Date:
21-Feb-00     Release date:   23-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P71454  (P71454_LEUME) -  D-alanine--D-alanine ligase 1
Seq:
Struc: 		377 a.a.
360 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.4  - D-alanine--D-alanine ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Peptidoglycan Biosynthesis (Part 1)
      Reaction: ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
ATP
 + 2 × D-alanine
 = ADP
 + phosphate
 + D-alanyl-D-alanine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell wall   2 terms 
  Biological process     cellular cell wall organization   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00129-5 Structure 8:463-470 (2000)
PubMed id: 10801495  
 
 
Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides.
A.P.Kuzin, T.Sun, J.Jorczak-Baillass, V.L.Healy, C.T.Walsh, J.R.Knox.
 
  ABSTRACT  
 
BACKGROUND: The bacterial cell wall and the enzymes that synthesize it are targets of glycopeptide antibiotics (vancomycins and teicoplanins) and beta-lactams (penicillins and cephalosporins). Biosynthesis of cell wall peptidoglycan requires a crosslinking of peptidyl moieties on adjacent glycan strands. The D-alanine-D-alanine transpeptidase, which catalyzes this crosslinking, is the target of beta-lactam antibiotics. Glycopeptides, in contrast, do not inhibit an enzyme, but bind directly to D-alanine-D-alanine and prevent subsequent crosslinking by the transpeptidase. Clinical resistance to vancomycin in enterococcal pathogens has been traced to altered ligases producing D-alanine-D-lactate rather than D-alanine-D-alanine. RESULTS: The structure of a D-alanine-D-lactate ligase has been determined by multiple anomalous dispersion (MAD) phasing to 2.4 A resolution. Co-crystallization of the Leuconostoc mesenteroides LmDdl2 ligase with ATP and a di-D-methylphosphinate produced ADP and a phosphinophosphate analog of the reaction intermediate of cell wall peptidoglycan biosynthesis. Comparison of this D-alanine-D-lactate ligase with the known structure of DdlB D-alanine-D-alanine ligase, a wild-type enzyme that does not provide vancomycin resistance, reveals alterations in the size and hydrophobicity of the site for D-lactate binding (subsite 2). A decrease was noted in the ability of the ligase to hydrogen bond a substrate molecule entering subsite 2. CONCLUSIONS: Structural differences at subsite 2 of the D-alanine-D-lactate ligase help explain a substrate specificity shift (D-alanine to D-lactate) leading to remodeled cell wall peptidoglycan and vancomycin resistance in Gram-positive pathogens.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Schematic showing the distances listed in Table 2. Residues Tyr255, Lys260 and Phe261 are on the omega loop. Gly322NH and Arg301 form an oxyanion hole.
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 463-470) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19456129 L.I.Robins, A.H.Williams, and C.R.Raetz (2009).
Structural basis for the sugar nucleotide and acyl-chain selectivity of Leptospira interrogans LpxA.
  Biochemistry, 48, 6191-6201.
PDB codes: 3hsq 3i3a 3i3x
19770507 Y.Kitamura, A.Ebihara, Y.Agari, A.Shinkai, K.Hirotsu, and S.Kuramitsu (2009).
Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions.
  Acta Crystallogr D Biol Crystallogr, 65, 1098-1106.  
18320587 D.Wu, L.Zhang, Y.Kong, J.Du, S.Chen, J.Chen, J.Ding, H.Jiang, and X.Shen (2008).
Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori.
  Proteins, 72, 1148-1160.
PDB code: 2pvp
18266853 H.Barreteau, A.Kovac, A.Boniface, M.Sova, S.Gobec, and D.Blanot (2008).
Cytoplasmic steps of peptidoglycan biosynthesis.
  FEMS Microbiol Rev, 32, 168-207.  
16779845 J.H.Lee, Y.Na, H.E.Song, D.Kim, B.H.Park, S.H.Rho, Y.J.Im, M.K.Kim, G.B.Kang, D.S.Lee, and S.H.Eom (2006).
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, 64, 1078-1082.
PDB code: 2fb9
16481318 M.E.Fraser, K.Hayakawa, M.S.Hume, D.G.Ryan, and E.R.Brownie (2006).
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
  J Biol Chem, 281, 11058-11065.
PDB codes: 2fp4 2fpg 2fpi 2fpp
16041744 J.Hiratake (2005).
Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications.
  Chem Rec, 5, 209-228.  
15477603 T.Hibi, H.Nii, T.Nakatsu, A.Kimura, H.Kato, J.Hiratake, and J.Oda (2004).
Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis.
  Proc Natl Acad Sci U S A, 101, 15052-15057.
PDB codes: 1v4g 1va6
11807177 J.Pootoolal, J.Neu, and G.D.Wright (2002).
Glycopeptide antibiotic resistance.
  Annu Rev Pharmacol Toxicol, 42, 381-408.  
10908650 D.I.Roper, T.Huyton, A.Vagin, and G.Dodson (2000).
The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA).
  Proc Natl Acad Sci U S A, 97, 8921-8925.
PDB code: 1e4e
  10801476 V.L.Healy, I.A.Lessard, D.I.Roper, J.R.Knox, and C.T.Walsh (2000).
Vancomycin resistance in enterococci: reprogramming of the D-ala-D-Ala ligases in bacterial peptidoglycan biosynthesis.
  Chem Biol, 7, R109-R119.  
10903933 V.L.Healy, L.S.Mullins, X.Li, S.E.Hall, F.M.Raushel, and C.T.Walsh (2000).
D-Ala-D-X ligases: evaluation of D-alanyl phosphate intermediate by MIX, PIX and rapid quench studies.
  Chem Biol, 7, 505-514.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.