NDLI: Homology modeling and docking studies of IscS from extremophile Acidithiobacillus ferrooxidans

Content Provider	Springer Nature Link
Author	Liu, Yuan dong Ding, Jian nan Qiu, Guan zhou Wang, Hai dong
Copyright Year	2007
Abstract	The gene iscS-3 from Acidithiobacillus ferrooxidans may play a central role in the delivery of sulfur to a variety of metabolic pathways in this organism. For insight into the sulfur metabolic mechanism of the bacteria, an integral three-dimensional (3D) molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and further used to search bind sites, carry out flexible docking with cofactor pyridoxal 5′-phosphate(PLP) and substrate cysteine and hereby detect its key residues. Through these procedures, the detail conformations of PLP-IscS(P-I) and cysteine-PLP-IscS(C-P-I) complexes were obtained. In P-I complex, the residues of Lys208, His106, Thr78, Ser205, His207, Asp182 and Gln185 have large interaction energies and/or hydrogen bonds fixation with PLP. In C-P-I complex, the amino group in cysteine is very near His106, Lys208 and PLP, the interaction energies for cysteine with them are very high. The above results are well consistent with those experimental facts of the homologues from other sources. Interestingly, the four residues of Glu105, Glu79, Ser203 and His180 in P-I docking and the residue of Lys213 in C-P-I docking also have great interaction energies, which are fitly conservation in IscSs from all kinds of sources but have not been identified before. From these results, this gene can be confirmed at 3D level to encode the iron-sulfur cluster assembly protein IscS and subsequently play a sulfur traffic role. Furthermore, the substrate cysteine can be presumed to be effectively recruited into the active site. Finally, the above detected key residues can be conjectured to be directly responsible for the bind and/or catalysis of PLP and cysteine.
Starting Page	742
Ending Page	749
Page Count	8
File Format	PDF
ISSN	10059784
Journal	Journal of Central South University of Technology
Volume Number	14
Issue Number	6
e-ISSN	19930666
Language	English
Publisher	Central South University of Technology
Publisher Date	2007-01-01
Publisher Place	Changsha
Access Restriction	Subscribed
Subject Keyword	bioleaching IscS Acidithiobacillus ferrooxidans homology modeling molecular dynamics docking pyridoxal 5′-phosphate(PLP) cysteine Engineering Metallic Materials
Content Type	Text
Resource Type	Article
Subject	Mechanics of Materials Materials Science Mechanical Engineering

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