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PDBsum entry 4me6

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protein ligands metals links
Ligase PDB id
4me6
Jmol
Contents
Protein chain
337 a.a.
Ligands
ADP
Metals
_MG
Waters ×171
PDB id:
4me6
Name: Ligase
Title: Crystal structure of d-alanine-d-alanine ligase a from xanth oryzae pathovar oryzae with adp
Structure: D-alanine--d-alanine ligase. Chain: a. Synonym: d-ala-d-ala ligase, d-alanylalanine synthetase. Engineered: yes. Mutation: yes
Source: Xanthomonas oryzae pv. Oryzae. Organism_taxid: 291331. Strain: kacc10331. Gene: ddla, ddl, xoo0352. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.198     R-free:   0.251
Authors: T.T.N.Doan,J.K.Kim,Y.J.Ahn,B.M.Lee,L.W.Kang
Key ref: T.T.Doan et al. (2014). Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides. Arch Biochem Biophys, 545, 92-99. PubMed id: 24440607 DOI: 10.1016/j.abb.2014.01.009
Date:
25-Aug-13     Release date:   19-Feb-14    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5H614  (Q5H614_XANOR) -  D-alanine--D-alanine ligase
Seq:
Struc:
347 a.a.
337 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 = ADP)
corresponds exactly
+ 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    
 
 
DOI no: 10.1016/j.abb.2014.01.009 Arch Biochem Biophys 545:92-99 (2014)
PubMed id: 24440607  
 
 
Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides.
T.T.Doan, J.K.Kim, H.P.Ngo, H.T.Tran, S.S.Cha, K.Min Chung, K.H.Huynh, Y.J.Ahn, L.W.Kang.
 
  ABSTRACT  
 
No abstract given.