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PDBsum entry 3r5f

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protein ligands metals links
Ligase PDB id
3r5f
Jmol
Contents
Protein chain
343 a.a.
Ligands
ATP
Metals
_MG
Waters ×125
PDB id:
3r5f
Name: Ligase
Title: Crystal structure of d-alanine-d-alnine ligase from xanthomo pv. Oryzae with atp
Structure: D-alanine--d-alanine ligase 1. Chain: a. Synonym: d-ala-d-ala ligase 1, d-alanylalanine synthetase 1 engineered: yes. Mutation: yes
Source: Xanthomonas oryzae pv. Oryzae. Organism_taxid: 291331. Strain: kacc10331. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.07Å     R-factor:   0.211     R-free:   0.277
Authors: T.T.N.Doan,J.K.Kim,L.W.Kang
Key ref: T.T.N.Doan et al. Crystal structure of d-Alanine-D-Alanine ligase a fro xanthomonas oryzae pathovar oryzae with atp. To be published, .
Date:
18-Mar-11     Release date:   25-May-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q2P8P8  (Q2P8P8_XANOM) -  D-alanine--D-alanine ligase
Seq:
Struc:
367 a.a.
343 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
Bound ligand (Het Group name = ATP)
corresponds exactly
+ 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     cell wall organization   3 terms 
  Biochemical function     catalytic activity     8 terms