To see full content of that page you need the activeISee plugin.
Get the latest version from here.

Structure of IDP01004

Dihydrodipicolinate synthase from Salmonella typhimurium LT2.

Edit deposit information
CSGID target
IDP01004 
PDB Id
3G0S (NCBI MMDB
Authors
J.Osipiuk,N.Maltseva,J.Stam,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jan 28, 2009 
Release Date
Feb 10, 2009 

Annotation

Description
Bacterial biosynthesis of lysine is a potential target for novel antibacterial agents as it provides both lysine for protein synthesis and meso-diaminopimelate for construction of the bacterial peptidoglycan cell wall. Dihydropicolinate synthase (DHDPS) catalyses the first reaction of (S)-lysine biosynthesis: an aldol condensation between (S)-aspartate -semialdehyde and pyruvate. The product of the reaction is the unstable heterocycle (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate (HTPA), which is thought to undergo a non-enzymatic dehydration to (S)-2,3-dihydrodipicolinate, the substrate of the next enzyme in the (S)-lysine biosynthetic pathway, DHDPR (dihydrodipicolinate reductase). The sequences of DHDPS from different sources are well-conserved. Almost all DHDPS enzymes with known structures are homotetramers formed as a dimer of tight dimers. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. A catalytic triad (Tyr133, Thr44, Tyr107 in E. coli), enabling a proton shuttle from the active site to bulk solvent, and the active site lysine is located in the barrel domain.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
CL CHLORIDE ION
GOL
MG MAGNESIUM ION

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=149.82Å, b=56.27Å, c=85.80Å
α=90.00, β=120.36, γ=90.00 
Solvent content
46.28  
Matthews coefficient
2.29  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
33.00-1.85Å (1.90-1.85Å)  
Rall(%)
15.7 
Rwork(%)
15.5 (30.9) 
Rfree(%)
19.0 (34.9) 
Num. observed reflections
50899 (3551) 
Num. Rfree reflections
2595 (201) 
Completeness(%)
96.8 (92.5) 

Model parameters

Num Atoms
5124  
Num Waters
544  
Num Hetatoms
0  
Model mean isotropic B factor
13.621Å2  
RMSD bond length
0.017Å  
RMSD bond angle
1.550°  
Filename uploaded
idp01004.pdb (uploaded on Feb 02, 2009 3:57 PM)  
Inserted
Feb 02, 2009