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PDBsum entry 3n8d

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
3n8d
Jmol
Contents
Protein chains
329 a.a. *
Ligands
ANP ×2
SO4 ×2
Metals
_CL
Waters ×272
* Residue conservation analysis
PDB id:
3n8d
Name: Ligase
Title: Crystal structure of staphylococcus aureus vrsa-9 d-ala:d-al
Structure: D-alanine--d-alanine ligase. Chain: a, b. Synonym: d-alanylalanine synthetase, d-ala-d-ala ligase. Engineered: yes. Mutation: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: vrsa-9. Gene: ddl. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.30Å     R-factor:   0.204     R-free:   0.276
Authors: F.A.Saul,A.Haouz,D.Meziane-Cherif
Key ref: D.Meziane-Cherif et al. (2010). Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9. J Bacteriol, 192, 5465-5471. PubMed id: 20729361
Date:
28-May-10     Release date:   13-Oct-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5HEB7  (DDL_STAAC) -  D-alanine--D-alanine ligase
Seq:
Struc:
356 a.a.
329 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
Bound ligand (Het Group name = ANP)
matches with 81.00% similarity
+ 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  

 

 
    reference    
 
 
J Bacteriol 192:5465-5471 (2010)
PubMed id: 20729361  
 
 
Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9.
D.Meziane-Cherif, F.A.Saul, C.Moubareck, P.Weber, A.Haouz, P.Courvalin, B.Périchon.
 
  ABSTRACT  
 
No abstract given.