1ney: Difference between revisions
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|PDB= 1ney |SIZE=350|CAPTION= <scene name='initialview01'>1ney</scene>, resolution 1.20Å | |PDB= 1ney |SIZE=350|CAPTION= <scene name='initialview01'>1ney</scene>, resolution 1.20Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene> | |LIGAND= <scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=FTR:FLUOROTRYPTOPHANE'>FTR</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </span> | ||
|GENE= TPI1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]) | |GENE= TPI1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1i45|1I45]], [[1nf0|1NF0]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ney FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ney OCA], [http://www.ebi.ac.uk/pdbsum/1ney PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ney RCSB]</span> | |||
}} | }} | ||
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[[Category: Rozovsky, S.]] | [[Category: Rozovsky, S.]] | ||
[[Category: Tong, L.]] | [[Category: Tong, L.]] | ||
[[Category: dhap]] | [[Category: dhap]] | ||
[[Category: dihydroxyacetone phosphate]] | [[Category: dihydroxyacetone phosphate]] | ||
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[[Category: yeast]] | [[Category: yeast]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:29:27 2008'' | ||
Revision as of 22:29, 30 March 2008
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| , resolution 1.20Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | TPI1 (Saccharomyces cerevisiae) | ||||||
| Activity: | Triose-phosphate isomerase, with EC number 5.3.1.1 | ||||||
| Related: | 1I45, 1NF0
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Triosephosphate Isomerase in Complex with DHAP
OverviewOverview
In enzyme catalysis, where exquisitely positioned functionality is the sine qua non, atomic coordinates for a Michaelis complex can provide powerful insights into activation of the substrate. We focus here on the initial proton transfer of the isomerization reaction catalyzed by triosephosphate isomerase and present the crystal structure of its Michaelis complex with the substrate dihydroxyacetone phosphate at near-atomic resolution. The active site is highly compact, with unusually short and bifurcated hydrogen bonds for both catalytic Glu-165 and His-95 residues. The carboxylate oxygen of the catalytic base Glu-165 is positioned in an unprecedented close interaction with the ketone and the alpha-hydroxy carbons of the substrate (C em leader O approximately 3.0 A), which is optimal for the proton transfer involving these centers. The electrophile that polarizes the substrate, His-95, has close contacts to the substrate's O1 and O2 (N em leader O < or = 3.0 and 2.6 A, respectively). The substrate is conformationally relaxed in the Michaelis complex: the phosphate group is out of the plane of the ketone group, and the hydroxy and ketone oxygen atoms are not in the cisoid configuration. The epsilon ammonium group of the electrophilic Lys-12 is within hydrogen-bonding distance of the substrate's ketone oxygen, the bridging oxygen, and a terminal phosphate's oxygen, suggesting a role for this residue in both catalysis and in controlling the flexibility of active-site loop.
About this StructureAbout this Structure
1NEY is a Single protein structure of sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.
ReferenceReference
Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution., Jogl G, Rozovsky S, McDermott AE, Tong L, Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):50-5. Epub 2002 Dec 30. PMID:12509510
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