3K3P

Crystal Structure of the Apo Form of D-Alanine:D-Alanine Ligase (DDl) from Streptococcus mutans

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the Apo form of D-Alanine:D-Alanine ligase (DDl) from Streptococcus mutans.

Lu, Y., Xu, H., Zhao, X.

(2010) Protein Pept Lett 17: 1053-1057

  • DOI: https://doi.org/10.2174/092986610791498858
  • Primary Citation of Related Structures:  
    3K3P

  • PubMed 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.

    • Organizational Affiliation: 

    West China Hospital Nanomedicine Laboratory, Center for Regenerative Medicine and Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital Sichuan University, Chengdu 610065, Sichuan, China.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanine--D-alanine ligase
A, B
383Streptococcus mutansMutation(s): 0 
Gene Names: ddl
EC: 6.3.2.4
UniProt
Find proteins for P95803 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore P95803 
Go to UniProtKB:  P95803
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95803
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.502α = 90
b = 79.502β = 90
c = 109.4γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2010-09-15 
    • Deposition Author(s): Lu, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-10-16
    Changes: Advisory, Data collection, Database references
  • Version 1.3: 2023-11-01
    Changes: Advisory, Data collection, Database references, Refinement description