2agk
From Proteopedia
(New page: 200px<br /><applet load="2agk" size="450" color="white" frame="true" align="right" spinBox="true" caption="2agk, resolution 1.300Å" /> '''Structure of S. cer...) |
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| - | [[Image:2agk.gif|left|200px]]<br /><applet load="2agk" size=" | + | [[Image:2agk.gif|left|200px]]<br /><applet load="2agk" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2agk, resolution 1.300Å" /> | caption="2agk, resolution 1.300Å" /> | ||
'''Structure of S. cerevisiae His6 protein'''<br /> | '''Structure of S. cerevisiae His6 protein'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The Saccharomyces cerevisiae His6 gene codes for the enzyme | + | The Saccharomyces cerevisiae His6 gene codes for the enzyme phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. To get an insight into the structure and function of this enzyme, we determined its X-ray structure at a resolution of 1.30 A using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 A wavelength. His6 folds in an (alpha/beta)8 barrel similar to HisA, which performs the same function in bacteria and archaea. We found a citrate molecule from the buffer bound in a pocket near the expected position of the active site and used it to model the open form of the substrate (phosphoribulosyl moiety), which is a reaction intermediate. This model enables us to identify catalytic residues and to propose a reaction mechanism where two aspartates act as acid/base catalysts: Asp134 as a proton donor for ring opening, and Asp9 as a proton acceptor and donor during enolization of the aminoaldose. Asp9 is conserved in yeast His6 and bacterial or archaeal HisA sequences, and Asp134 has equivalents in both HisA and TrpF, but they occur at a different position in the protein sequence. |
==About this Structure== | ==About this Structure== | ||
| - | 2AGK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with CL, CIT and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/1-(5-phosphoribosyl)-5-_((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide_isomerase 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.16 5.3.1.16] Full crystallographic information is available from [http:// | + | 2AGK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=CIT:'>CIT</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/1-(5-phosphoribosyl)-5-_((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide_isomerase 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.16 5.3.1.16] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AGK OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Tilbeurgh, H | + | [[Category: Tilbeurgh, H V.]] |
| - | [[Category: YSG, Paris-Sud | + | [[Category: YSG, Paris-Sud Yeast Structural Genomics.]] |
[[Category: CIT]] | [[Category: CIT]] | ||
[[Category: CL]] | [[Category: CL]] | ||
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[[Category: ysg]] | [[Category: ysg]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:27:11 2008'' |
Revision as of 14:27, 21 February 2008
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Structure of S. cerevisiae His6 protein
Overview
The Saccharomyces cerevisiae His6 gene codes for the enzyme phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. To get an insight into the structure and function of this enzyme, we determined its X-ray structure at a resolution of 1.30 A using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 A wavelength. His6 folds in an (alpha/beta)8 barrel similar to HisA, which performs the same function in bacteria and archaea. We found a citrate molecule from the buffer bound in a pocket near the expected position of the active site and used it to model the open form of the substrate (phosphoribulosyl moiety), which is a reaction intermediate. This model enables us to identify catalytic residues and to propose a reaction mechanism where two aspartates act as acid/base catalysts: Asp134 as a proton donor for ring opening, and Asp9 as a proton acceptor and donor during enolization of the aminoaldose. Asp9 is conserved in yeast His6 and bacterial or archaeal HisA sequences, and Asp134 has equivalents in both HisA and TrpF, but they occur at a different position in the protein sequence.
About this Structure
2AGK is a Single protein structure of sequence from Saccharomyces cerevisiae with , and as ligands. Active as 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase, with EC number 5.3.1.16 Full crystallographic information is available from OCA.
Reference
Crystal structure of the yeast His6 enzyme suggests a reaction mechanism., Quevillon-Cheruel S, Leulliot N, Graille M, Blondeau K, Janin J, van Tilbeurgh H, Protein Sci. 2006 Jun;15(6):1516-21. PMID:16731983
Page seeded by OCA on Thu Feb 21 16:27:11 2008
Categories: 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | Saccharomyces cerevisiae | Single protein | Tilbeurgh, H V. | YSG, Paris-Sud Yeast Structural Genomics. | CIT | CL | EDO | Paris-sud yeast structural genomics | S. cerevisiae structural genomics project | Structural genomics | Tim alpha/beta barrel | Ysg
