Annotation

Description

Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyzes the succinyl-CoA-dependent acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate as part of the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. This pathway provides meso-diaminopimelate as a building block for cell wall peptidoglycan in most bacteria, and is regarded as a target pathway for antibacterial agents. In this 1.8A DapD structure from Yersinia pestis, there are three molecules form the trimer in the assymetric unit. 

Functional assignment

Tetrahydrodipicolinate N-succinyltransferase (DapD) 

Structure information

Unit cell parameters

Space Group

P 1 21 1  

Unit Cell

a=57.79Å, b=69.69Å, c=106.45Å
α=90.00, β=105.28, γ=90.00 

Solvent content

46.14  

Matthews coefficient

2.28  

Refinement

Data for the highest resolution shell is in parentheses.

Resolution range

57.64-1.80Å (1.85-1.80Å)  

R_all(%)

23.0 

R_work(%)

22.7 (26.7) 

R_free(%)

27.2 (30.8) 

Num. observed reflections

74324 (5013) 

Num. R_free reflections

3716 (263) 

Completeness(%)

98.2 (90.2) 

Model parameters

Num Atoms

6574  

Num Waters

285  

Num Hetatoms

0  

Model mean isotropic B factor

16.960Ų  

RMSD bond length

0.022Å  

RMSD bond angle

1.830°  

Filename uploaded

IDP571_2pdb.pdb (uploaded on May 04, 2009 5:52 PM)  

Inserted

May 04, 2009