spacer
spacer

PDBsum entry 3k3p

Go to PDB code: 
protein Protein-protein interface(s) links
Ligase PDB id
3k3p
Jmol
Contents
Protein chains
317 a.a. *
Waters ×150
* Residue conservation analysis
PDB id:
3k3p
Name: Ligase
Title: Crystal structure of the apo form of d-alanine:d-alanine lig from streptococcus mutans
Structure: D-alanine--d-alanine ligase. Chain: a, b. Synonym: d-alanylalanine synthetase, d-ala-d-ala ligase. Engineered: yes
Source: Streptococcus mutans. Organism_taxid: 1309. Strain: ua159. Gene: ddl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.23Å     R-factor:   0.199     R-free:   0.248
Authors: Y.Lu
Key ref: Y.Lu et al. (2010). Crystal structure of the Apo form of D-Alanine:D-Alanine ligase (DDl) from Streptococcus mutans. Protein Pept Lett, 17, 1053-1057. PubMed id: 20522004
Date:
03-Oct-09     Release date:   15-Sep-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P95803  (DDL_STRMU) -  D-alanine--D-alanine ligase
Seq:
Struc:
349 a.a.
317 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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     cytoplasm   1 term 
  Biological process     regulation of cell shape   2 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
Protein Pept Lett 17:1053-1057 (2010)
PubMed id: 20522004  
 
 
Crystal structure of the Apo form of D-Alanine:D-Alanine ligase (DDl) from Streptococcus mutans.
Y.Lu, H.Xu, X.Zhao.
 
  ABSTRACT  
 
D-Alanine:D-Alanine ligase (DDl) catalyzes the formation of D-Alanine:D-Alanine dipeptide and is an essential enzyme in bacterial cell wall biosynthesis.. This enzyme does not have a human ortholog, making it an attractive target for developing new antibiotic drugs. We determined the crystal structure at 2.23 A resolution of DDl from Streptococcus mutans (SmDDl), the principal aetiological agent of human dental caries. This structure reveals that SmDDl is a dimer and has a disordered omega-loop region.