|Table of Contents|

Homology Modeling for Sulfur Oxygenase/Reductase(PDF)

Chinese Journal of Applied & Environmental Biology[ISSN:1006-687X/CN:51-1482/Q]

Issue:
2010 03
Page:
424-428
Research Field:
T & M
Publishing date:

Info

Title:
Homology Modeling for Sulfur Oxygenase/Reductase
Author(s):
MENG Zhen YOU Xiaoyan JIANG Chengying MA Juncai
(1State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China)
(2Scientific Data Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China)
Keywords:
homology modeling evaluation of models sulfur oxygenase/reductase
CLC:
Q554
PACS:
DOI:
10.3724/SP.J.1145.2010.00424
DocumentCode:

Abstract:
Sulfur oxygenase/reductase (SOR) plays a key role in oxidative metabolism of sulfur acid by thermophilic archaea. Its catalytic mechanism and molecular engineering are concerned widely. In this paper, the modeling and evaluation of the subunits of SORs were processed. The steps of homology modeling are as follows: 1) Search of protein sequence similarity; 2) alignment of sequence and structure ; 3) initial modeling; 4) simulation of refinement and molecular dynamics (MD); and 5) evaluation of the optimized model. This paper also discusses the modeling, evaluation and characterized data for SORs.
Fig 3, Tab 4, Ref 19

References

1 Emmel T, Sand W, Konig WA, Bock E. Evidence for the existence of a sulfur oxygenase in Sulfolobus brierleyi. J Gen Microbiol, 1986, 132: 3415~3420
2 He ZG, Li YQ, Zhou PJ, Liu SJ. Cloning and heterologous expression of a sulfur oxygenase/reductase gene from the thermoacidophilic archaeon Acidianus sp. S5 in Escherichia coli. FEMS Microbiol Lett, 2000, 193 (2): 217~221
3 He ZG, Zhong HF, Li YQ. Acidianus tengchongensis sp. nov., a new species of acidothermophilic archaeon isolated from an acidothermal spring. Curr Microbiol, 2004, 48 (2): 159~163
4 Sun CW, Chen ZW, He ZG, Zhou PJ, Liu SJ. Purification and properties of the sulfur oxygenase/reductase from the acidothermophilic archaeon, Acidianus strain S5. Extremophiles, 2003, 7 (2): 131~134
5 Kletzin A. Coupled enzymatic production of sulfite, thiosulfate, and hydrogen sulfide from sulfur: Purification and properties of asulfur oxygenase reductase from the facultatively anaerobic archaebacterium Desulfurolobus ambivalens. J Bacteriol, 1989, 171 (3): 1638~1643
6 Kletzin A. Molecular characterization of the sor gene, which encodes the sulfur oxygenase/reductase of the thermoacidophilic Archaeum Desulfurolobus ambivalens. J Bacteriol, 1992, 174 (18): 5854~5859
7 Bathe S. Norris PR. Ferrous iron- and sulfur-induced genes in Sulfolobus metallicus. Appl Environ Microbiol, 2007 73 (8): 2491~2497
8 Liu SJ. Archaeal and bacterial sulfur oxygenase reductase: Genetic diversity and physiological function. In: Dahl C, Friedrich CG eds. Microbial Sulfur Metabolism. Heidelberg, Germany: Springer, 2008. 217~224
9 Urich T, Cláudio M. Gomes, Arnulf Kletzin, Carlos Frazão. X-ray structure of a self-compartmentalizing sulfur cycle metalloenzyme. Science, 2006, 311: 996~1000
10 Li M, Chen ZW, Zhang PF, Pan XW, Jiang CY, An XM, Liu SJ, Chang WR. Crystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis. Biochem Biophys Res Commun, 2008, 369 (3): 919~923
11 Chen ZW, Jiang CY, Liu SJ. Site-directed mutagenesis reveals new and essential elements for iron-coordination of the sulfur oxygenase reductase from the acidothermophilic Acidianus tengchongensis. Chin Sci Bull, 2009, 54 (1): 41~45
12 Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 1994, 22: 4673-4680
13 Petrey D, Honig B. GRASP2: Visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol, 2003, 374: 492~509
14 Fiser A, Sali A. Modeller: Generation and refinement of homology-based protein structure models. Methods Enzymol, 2003, 437: 461~491
15 Laskowski RA, MacArthur MW, Moss DS, Thornton JM, PROCHECK: A program to check the stereo chemical quality of protein structures. J Appl Cryst, 1993, 26: 283~291
16 Wiederstein M, Sippl MJ. ProSA-Web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res, 2007, 35: W407~W410
17 Sippl MJ. Recognition of Errors in three-dimensional structures of proteins. Proteins, 1993, 17: 355~362
18 Vriend G. WHAT IF: A molecular modeling and drug design program. J Mol Graph, 1990, 8 (1): 52~56
19 Zheng ZL, Zou ZY, Liu ZG, Tsai KC, Liu AF, Zou GL. Construction of a 3D model of nattokinase, a novel fibrinolytic enzyme from Bacillus natto: A novel nucleophilic catalytic mechanism for nattokinase. J Mol Graphics Modell, 2005, 23 (4): 373~380

Memo

Memo:
-
Last Update: 2010-06-23