2agk
From Proteopedia
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|PDB= 2agk |SIZE=350|CAPTION= <scene name='initialview01'>2agk</scene>, resolution 1.300Å | |PDB= 2agk |SIZE=350|CAPTION= <scene name='initialview01'>2agk</scene>, resolution 1.300Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= YIL020c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]) | |GENE= YIL020c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2agk OCA], [http://www.ebi.ac.uk/pdbsum/2agk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2agk RCSB]</span> | ||
}} | }} | ||
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[[Category: Tilbeurgh, H V.]] | [[Category: Tilbeurgh, H V.]] | ||
[[Category: YSG, Paris-Sud Yeast Structural Genomics.]] | [[Category: YSG, Paris-Sud Yeast Structural Genomics.]] | ||
| - | [[Category: CIT]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: EDO]] | ||
[[Category: paris-sud yeast structural genomic]] | [[Category: paris-sud yeast structural genomic]] | ||
[[Category: s. cerevisiae structural genomics project]] | [[Category: s. cerevisiae structural genomics project]] | ||
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[[Category: ysg]] | [[Category: ysg]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:52:24 2008'' |
Revision as of 22:52, 30 March 2008
| |||||||
| , resolution 1.300Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | YIL020c (Saccharomyces cerevisiae) | ||||||
| Activity: | 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase, with EC number 5.3.1.16 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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 Mon Mar 31 01:52:24 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. | Paris-sud yeast structural genomic | S. cerevisiae structural genomics project | Structural genomic | Tim alpha/beta barrel | Ysg
