PDBsum entry 2i87

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Ligase PDB id
Jmol PyMol
Protein chains
345 a.a. *
SO4 ×2
Waters ×91
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Allosteric inhibition of staphylococcus aureus d-alanine:d-a ligase revealed by crystallographic studies
Structure: D-alanine-d-alanine ligase. Chain: a, b. Synonym: d-alanylalanine synthetase, d-ala-d-ala ligase. Engineered: yes
Source: Staphylococcus aureus subsp. Aureus. Organism_taxid: 93062. Strain: col. Gene: ddl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.202     R-free:   0.241
Authors: S.Liu,J.S.Chang,J.T.Herberg,M.Horng,P.K.Tomich,A.H.Lin,K.R.M
Key ref:
S.Liu et al. (2006). Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies. Proc Natl Acad Sci U S A, 103, 15178-15183. PubMed id: 17015835 DOI: 10.1073/pnas.0604905103
01-Sep-06     Release date:   03-Oct-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q5HEB7  (DDL_STAAC) -  D-alanine--D-alanine ligase
356 a.a.
345 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

Peptidoglycan Biosynthesis (Part 1)
      Reaction: ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
+ 2 × D-alanine
+ 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     cytoplasm   1 term 
  Biological process     cell wall organization   3 terms 
  Biochemical function     nucleotide binding     5 terms  


DOI no: 10.1073/pnas.0604905103 Proc Natl Acad Sci U S A 103:15178-15183 (2006)
PubMed id: 17015835  
Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies.
S.Liu, J.S.Chang, J.T.Herberg, M.M.Horng, P.K.Tomich, A.H.Lin, K.R.Marotti.
D-alanine:D-alanine ligase (DDl) is an essential enzyme in bacterial cell wall biosynthesis and an important target for developing new antibiotics. It catalyzes the formation of D-alanine:D-alanine dipeptide, sequentially by using one D-alanine and one ATP as substrates for the first-half reaction, and a second D-alanine substrate to complete the reaction. Some gain of function DDl mutants can use an alternate second substrate, causing resistance to vancomycin, one of the last lines of defense against life-threatening Gram-positive infections. Here, we report the crystal structure of Staphylococcus aureus DDl (StaDDl) and its cocrystal structures with 3-chloro-2,2-dimethyl-N-[4(trifluoromethyl)phenyl]propanamide (inhibitor 1) (Ki=4 microM against StaDDl) and with ADP, one of the reaction products, at resolutions of 2.0, 2.2, and 2.6 A, respectively. The overall structure of StaDDl can be divided into three distinct domains. The inhibitor binds to a hydrophobic pocket at the interface of the first and the third domain. This inhibitor-binding pocket is adjacent to the first D-alanine substrate site but does not overlap with any substrate sites. An allosteric inhibition mechanism of StaDDl by this compound was proposed. The mechanism provides the basis for developing new antibiotics targeting D-alanine:D-alanine ligase. Because this compound only interacts with residues from the first D-alanine site, inhibitors with this binding mode potentially could overcome vancomycin resistance.
  Selected figure(s)  
Figure 3.
Fig. 3. A composite surface representation of StaDDl ligand-binding sites. The electrostatic protein surface was constructed from apo StaDDl structure, with red and blue representing negative and positive charges, respectively, white is for neutral. Ligands are in stick model. ADP and the first Mg^2+ (Mg1) are from ADP+Mg^2+-bound StaDDl structure. The phosphorylated phosphinate and the second Mg^2+ (Mg2) are modeled in from substrates bound LmDDl2 monomer by superimposition by using program LSQMAN (20). Inhibitor 1 is from inhibitor 1–StaDDl complex. For clarity, the carbon atoms of ADP, phosphinate, and inhibitor 1 are shown in cyan, yellow, and magenta color, respectively.
Figure 5.
Fig. 5. Structure superposition of inhibitor 1-bound StaDDl with reaction intermediate analog bound LmDDl2. Residues essential for the first half-reaction are labeled (see text). For clarity, carbon atoms of StaDDl, inhibitor 1, and phosphinate are colored cyan, magenta, and white, respectively.
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20729361 D.Meziane-Cherif, F.A.Saul, C.Moubareck, P.Weber, A.Haouz, P.Courvalin, and B.Périchon (2010).
Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9.
  J Bacteriol, 192, 5465-5471.
PDB code: 3n8d
19528271 C.Moubareck, D.Meziane-Cherif, P.Courvalin, and B.Périchon (2009).
VanA-type Staphylococcus aureus strain VRSA-7 is partially dependent on vancomycin for growth.
  Antimicrob Agents Chemother, 53, 3657-3663.  
19546371 K.Kurokawa, H.Hamamoto, M.Matsuo, S.Nishida, N.Yamane, B.L.Lee, K.Murakami, H.Maki, and K.Sekimizu (2009).
Evaluation of target specificity of antibacterial agents using Staphylococcus aureus ddlA mutants and D-cycloserine in a silkworm infection model.
  Antimicrob Agents Chemother, 53, 4025-4027.  
19362848 S.M.Firestine, H.Paritala, J.E.McDonnell, J.B.Thoden, and H.M.Holden (2009).
Identification of inhibitors of N5-carboxyaminoimidazole ribonucleotide synthetase by high-throughput screening.
  Bioorg Med Chem, 17, 3317-3323.  
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.  
18519725 A.A.Miller, G.L.Bundy, J.E.Mott, J.E.Skepner, T.P.Boyle, D.W.Harris, A.E.Hromockyj, K.R.Marotti, G.E.Zurenko, J.B.Munzner, M.T.Sweeney, G.F.Bammert, J.C.Hamel, C.W.Ford, W.Z.Zhong, D.R.Graber, G.E.Martin, F.Han, L.A.Dolak, E.P.Seest, J.C.Ruble, G.M.Kamilar, J.R.Palmer, L.S.Banitt, A.R.Hurd, and M.R.Barbachyn (2008).
Discovery and characterization of QPT-1, the progenitor of a new class of bacterial topoisomerase inhibitors.
  Antimicrob Agents Chemother, 52, 2806-2812.  
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.  
  19052362 T.T.Doan, J.K.Kim, H.Kim, Y.J.Ahn, J.G.Kim, B.M.Lee, and L.W.Kang (2008).
Expression, crystallization and preliminary X-ray crystallographic analysis of Xoo0352, D-alanine-D-alanine ligase A, from Xanthomonas oryzae pv. oryzae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1115-1117.  
18041906 K.Ohlsen, and U.Lorenz (2007).
Novel targets for antibiotics in Staphylococcus aureus.
  Future Microbiol, 2, 655-666.  
  17768361 Y.Z.Lu, Y.Sheng, L.F.Li, D.W.Tang, X.Y.Liu, X.Zhao, Y.H.Liang, and X.D.Su (2007).
Crystallization and preliminary crystallographic analysis of D-alanine-D-alanine ligase from Streptococcus mutans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 807-808.  
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 code is shown on the right.