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Title

Homology modeling of Ferredoxin-nitrite reductase from Arabidopsis thaliana


 

Authors

Karim Kherraz*, Khaled Kherraz, Abdelkrim Kameli
 

Affiliation

Biology department, Ecole Normale Superieure, ENS-Kouba, PB 92, Algiers, Algeria

 

Email

karimkherraz12@yahoo.fr; *Corresponding author

Phone

+213557710828

Article Type

Hypothesis

 

Date

Received December 02, 2010; Accepted December 24, 2010; Published April 22, 2011

 

Abstract

Nitrogen is one of the major growth-limiting nutrients for plants: The main source of nitrogen in most of the higher plants is nitrate taken up through roots. Nitrate can be reduced both in the chloroplasts (photosynthetic tissues) and in proplastes (nonphotosynthetic tissues) such as roots. Ferredoxin-nitrite reductase (NiR) catalyses the reduction of nitrite to ammonium in the second step of the nitrate- assimilation pathway. Homology model of Ferredoxin-nitrite reductase has been constructed using the X-ray structure (PDB code: 2akj) a s a template and MODELLER 9v5 software. The resulting model assessed by PROCHECK, PROSAII and RMSD that showed the final refined model is reliable: has 81% of amino acid sequence identity with template, 0.2 as RMSD and has (-10.37) as Z-scores, the Ramachandran plot analysis showed that conformations for 99.5 % of amino acid residues are within the most favored regions. The model could prove useful in further functional characterization of this protein.
 

Keywords

Arabidopsis thaliana; Homology modeling; Validation.

Citation

Kherraz et al. Bioinformation 6(3): 115-119 (2011)

Edited by

I Roterman

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.