Full structure building and docking of NifS from extremophile Acidithiobacillus ferrooxidans

• Published in: Transactions of Nonferrous Metals Society of China Vol. 18; no. 4; pp. 995 - 1002
• Main Author: 刘元东 邱冠周 王海东 蒋莹 张成桂 夏乐先
• Format: Journal Article
• Language: English
• Published: Elsevier Ltd 01.08.2008; School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
• Subjects: Acidithiobacillus ferrooxidans; bioleaching; cysteine; docking; homology modeling; molecular dynamics; NifS; pyridoxal 5′-phosphate(PLP); 分子动力学; 半胱氨酸; 固氮基因; 固氮酶; Acidithiobacillus ferrooxidans; docking; pyridoxal 5′-phosphate(PLP); homology modeling; cysteine; bioleaching; molecular dynamics; NifS
• ISSN: 1003-6326
• DOI: 10.1016/S1003-6326(08)60171-5

The gene iscS-2 from extremophile Acidithiobacillus ferrooxidans may play a crucial role in nitrogenase maturation. To investigate the protein encoded by this gene, a reliable integral three-dimensional molecular structure was built. The obtained structure was further used to search binding sites, carry out the flexible docking with cofactor pyridoxal 5＇-phosphate（PLP） and substrate cysteine, and identify its key residues. The docking results of PLP reveal that the residues of Lys203, His100, Thr73, Ser200, His202, Asp177 and GlnlS0 have large interaction energies and/or hydrogen bonds fixation with PLP. The docking results of cysteine show that the amino group in cysteine is very near His100, Lys203 and PLP, and the interaction energies for cysteine with them are very big. These identified residues are in line with the experimental facts of NifS from other sources. Moreover, the four residues of Asn152, Val179, Ala102 and Met148 in the PLP docking and the two residues of Lys208 and Alal02 in the cysteine docking also have large interaction energies, which are fitly conserved in NifS from all kinds of sources but have not been identified before, According to these results, this gene encodes NifS protein, and the substrate cysteine can be effectively recruited into the active site. Furthermore, all of the above detected key residues are directly responsible for the binding and/or catalysis of PLP and cysteine.