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Structure of IDP90844

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion

Edit deposit information
CSGID target
IDP90844 
PDB Id
3P52 (NCBI MMDB
Authors
E.V.Filippova,Z.Wawrzak,O.Onopriyenko,T.Skarina,A.Edwards,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Ekaterina Filippova 
Responsible lab
Northwestern University 
Deposition Date
Oct 07, 2010 
Release Date
Oct 27, 2010 

Annotation

Description
The NH(3)-dependent NAD(+) synthetase (NADS, gene nadE) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD(+). This enzyme is conserved in nearly all bacterial pathogens and a promising drug target for the development of new antibiotics. The crystal structure of NADS from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion was determined at 2.74 A resolution. The structure accommodates a tight homodimer with a remarkable alpha/beta subunit topology. The major loop (178-196) that has a role in substrate recognition and stabilization, in addition to the protection of the reaction intermediate is disordered in the active site in both subunits of the dimer molecule. The nitrate ion is found in a splay between strands b1 and b2 where adenine group of AMP molecule is bound for catalysis in structures of known NADS. Our data is the first to suggest the nitrate ion binding site in NADS enzymes. 
Functional assignment
biosynthesis of nicotinamide adenine dinucleotide 

Ligands

Ligand code Name Ligand type
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 3 2 1  
Unit Cell

a=120.94Å, b=120.94Å, c=91.80Å
α=90.00, β=90.00, γ=120.00 
Solvent content
64.34  
Matthews coefficient
3.45  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.00-2.74Å (2.81-2.74Å)  
Rall(%)
21.1 
Rwork(%)
20.9 (29.8) 
Rfree(%)
24.5 (34.2) 
Num. observed reflections
20619 (1467) 
Num. Rfree reflections
1051 (75) 
Completeness(%)
99.2 (95.5) 

Model parameters

Num Atoms
3465  
Num Waters
65  
Num Hetatoms
194  
Model mean isotropic B factor
72.080Å2  
RMSD bond length
0.016Å  
RMSD bond angle
1.653°  
Filename uploaded
rcsb061965.pdb (uploaded on Oct 11, 2010 11:43 AM)  
Inserted
Oct 11, 2010