Sandbox 4

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{{Seed}}
 
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[[Image:1tsj.png|left|200px]]
 
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The line below this paragraph, containing "STRUCTURE_1tsj", creates the "Structure Box" on the page.
 
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
 
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=Crystal structure of protein from Staphylococcus aureus=
 
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PDB entry 1tsj refers to a hypothetical protein of 139 residues which is a predicted dimer<ref> Henrick, K., and Thornton, J.M. (1998). PQS: a protein quaternary structure file server. Trends Biochem. Sci. 23, 358- 361.</ref> and predicted as a cytoplasmic protein.<ref> Bhasin, M., Garg, A. and Raghava, GPS (2005) PSLpred: prediction of subcellular localization of bacterial proteins. Bioinformatics. 21, 2522-2524.
 
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Gardy JL, Spencer C, Wang K, Ester M, Tusn?dy GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS. (2003) PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res. 31, 3613-3617.
 
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Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner. (2003). Predicting Subcellular Localization of Proteins using Machine-Learned Classifiers. Bioinformatics. 20, 547-556.
 
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Hua S, Sun Z. (2001). Support vector machine approach for protein subcellular localization prediction. Bioinformatics. 17, 721-728.</ref>
 
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The protein is associated with Pfam<ref>Finn R, Griffiths-Jones S, Bateman A. (2003). Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. Chapter 2: Unit 2.5.</ref> entry PF06983 of 3-demethylubiquinone-9 3-methyltransferases.
The protein is associated with Pfam<ref>Finn R, Griffiths-Jones S, Bateman A. (2003). Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. Chapter 2: Unit 2.5.</ref> entry PF06983 of 3-demethylubiquinone-9 3-methyltransferases.
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Among the sequence homologs found by PSI-Blast<ref> Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.</ref> there are the predicted 3-demethylubiquinone-9 3-methyltransferase proteins Q192X9 from Desulfitobacterium hafniense and A9VFW6 from Bacillus weihenstephanensis. Its potential substrate is S-adenosyl-L-methionine with the formal charge +1.
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<applet load='1tsj' size='400' frame='true' align='right' caption='1tsj, resolution 2.60Å' /> <scene name='1tsj/Evolutionary_consevation_1tsj/1'>highly preserved</scene> and negatively charged.
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PDB entry [[2rk9]] was found to be structurally<ref> Arnold K, Kiefer F, Kopp J, Battey JN, Podvinec M, Westbrook JD, Berman HM, Bordoli L, Schwede T. (2008). The Protein Model Portal. J Struct Funct Genomics.</ref> similar to the query protein Q8NX24 and share a significant sequence similarity<ref> Emmert D.B., Stoehr P.J., Stoesser G., Cameron G.N. (1994). The European Bioinformatics Institute (EBI) databases. Nucleic Acids Res. 26, 3445-3449.</ref> of 21.0%. This structure homolog is an Oxidoreductase from Vibrio Splendidus and binds methylglyoxal which is not charged. Another structural similarity was found with PDB entry [[1t47]] which is a 4-hydroxyphenylpyruvate dioxygenase, but the sequence similarity is lower (7.7%).
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[[Image:Chimera 1tsjA 2rk9B.png|thumb|350px|right|Superimposition between chain A of Q8NX24 (orange) and chain B of 2rk9 (green). The arrow indicates the active site of 2rk9.]]
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Both the sequence and structure homologs are from the same superfamily titled 'Glyoxalase/bleomycin resistance protein/dioxygenase'. The Superimposition<ref> Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. (2004). UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612.</ref> between chain A of Q8NX24 (orange) and chain B of 2rk9 (green) shows that the proteins indeed have similar folds.
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It seems that the chosen active site of Q8NX24 is the largest cavity found on the protein's surface, in most cases this cavity is the functional area.<ref> J. Liang, H. Edelsbrunner, and C. Woodward, (1998). Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7, 1884–1897.</ref> Evidence approving this choice is that the superimpositions with 2rk9 placed its known active site<ref> Thornalley P.J., (2003). Glyoxalase I – structure, function and a critical role in the enzymatic defence against glycation. Biochemical Soc Trans. 31, 1343-1348.</ref> at the same location.
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The electrostatic potential<ref>Sanner, M.F. (1999). Python: a programming language for software integration and development. J. Mol. Graph. Model. 17, 57-61.</ref> on the protein's surface is mostly negative.
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[[Image:Electrostatic potential 1tsj.PNG|thumb|350px|none|The electrostatic potential of Q8NX24. The figure was produced with Python Molecular Viewer.]]
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According to the evolutionary conservation<ref>Goldenberg O, Erez E, Nimrod G, Ben-Tal N. (2009). The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res. 37, D323-327.</ref> the potential catalytic area is <applet load='1tsj' size='400' frame='true' align='right' caption='1tsj, resolution 2.60Å' /> <scene name='1tsj/Evolutionary_consevation_1tsj/1'>highly preserved</scene> and negatively charged.
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<center>{{Template:ColorKey_ConSurf}}</center>
<center>{{Template:ColorKey_ConSurf}}</center>
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==References==
==References==
<references/>
<references/>
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[[Category: Staphylococcus aureus subsp. aureus]]
 
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[[Category: Burley, S K.]]
 
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[[Category: Gorman, J.]]
 
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[[Category: Min, T.]]
 
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[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
 
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[[Category: Shapiro, L.]]
 
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[[Category: Conserved hypothetical protein]]
 
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[[Category: Crystal structure]]
 
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[[Category: New york structural genomics consortium]]
 
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[[Category: New york structural genomix research consortium]]
 
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[[Category: Nysgxrc]]
 
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[[Category: Protein structure initiative]]
 
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[[Category: Psi]]
 
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[[Category: Structural genomic]]
 

Revision as of 16:54, 18 February 2009

The protein is associated with Pfam[1] entry PF06983 of 3-demethylubiquinone-9 3-methyltransferases.

1tsj, resolution 2.60Å

Drag the structure with the mouse to rotate
and negatively charged.
Image:Consurf_key_small.gif


The potential substrate S-adenosyl-L-methionine has positive formal charge which fits the negative electrostatic potential in the potential catalytic area. The alternative substrate found by the structural homology methylglyoxal is not charged and thus less probable to attach to the potential catalytic area.

It seems more likely that Q8NX24 belongs to the Glyoxalase/bleomycin resistance protein/dioxygenase superfamily and functions as a demethylubiquinone-9 3-methyltransferase protein.


References

  1. ↑ Finn R, Griffiths-Jones S, Bateman A. (2003). Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. Chapter 2: Unit 2.5.
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