PDBsum entry 2fb9

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protein links
Ligase PDB id
Protein chain
322 a.a. *
Waters ×115
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Crystal structure of the apo form of d-alanine: d-alanine li from thermus caldophilus: a basis for the substrate-induced conformational changes
Structure: D-alanine:d-alanine ligase. Chain: a. Engineered: yes
Source: Thermus caldophilus. Organism_taxid: 272. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.90Å     R-factor:   0.228     R-free:   0.268
Authors: J.H.Lee,Y.Na,S.H.Eom
Key ref:
J.H.Lee et al. (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. PubMed id: 16779845 DOI: 10.1002/prot.20927
08-Dec-05     Release date:   29-Aug-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q3T920  (Q3T920_THECA) -  D-alanine--D-alanine ligase
319 a.a.
322 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     catalytic activity     8 terms  


DOI no: 10.1002/prot.20927 Proteins 64:1078-1082 (2006)
PubMed id: 16779845  
Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes.
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, S.H.Eom.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. Crystal structure of Tca Ddl. A: Ribbon diagram showing the overall structure of the Tca Ddl protein. The -helices are labeled 1- 9, and -strands are labeled 1- 13. B: Multiple sequence alignment of D-alanine:D-alanine ligase from Thermus caldophilus (Tca Ddl), D-alanine:D-alanine ligase from Escherichia coli (Eco DdlB), D-alanine:D-lactate ligase from Leuconostoc mesenteroides (Lme D-Ala:D-Lac ligase) and D-alanine:D-lactate ligase from Enterococcus faecium (Efa VanA) using ClustalX.[22] Highly conserved residues are shaded in black and gray. C: Ribbon diagram of the Tca Ddl dimer. -Helices situated within the dimer interface [ 3 (violet), 4 (yellow), and 5 (red)] are indicated and labeled 3 , 4 , and 5 in the opposing subunit.
Figure 2.
Figure 2. Comparison of the open and closed conformations of Ddl. A: A stereoview of the superposition of the structures of Tca Ddl (slate blue), Eco DdlB (yellow, PDB ID: 2DLN), Lme D-Ala:D-Lac ligase (green, PDB ID: 1EHI) and Efa VanA (violet, PDB ID: 1E4E). B: Stereoview of the superposition of Tca Ddl (open form: slate blue) and Eco DdlB (closed form: yellow) complexed with ATP (violet) and phosphorylated phosphinate (green: labeled as PHY). The swing motion (about 16 Å) of lid loop and the rotation (about 17°) of central domain (red dotted circle) may induce the closed conformation. Lys215 and Tyr216 on a mobile lid loop make hydrogen bonds with Ser150 and Ser151, respectively, on a central domain, which fixes the lid loop so that it covers the substrate binding site in the closed conformation.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 64, 1078-1082) copyright 2006.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
  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.