3b9x

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(New page: 200px {{Structure |PDB= 3b9x |SIZE=350|CAPTION= <scene name='initialview01'>3b9x</scene>, resolution 2.30&Aring; |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+F...)
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[[Image:3b9x.jpg|left|200px]]
[[Image:3b9x.jpg|left|200px]]
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{{Structure
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|PDB= 3b9x |SIZE=350|CAPTION= <scene name='initialview01'>3b9x</scene>, resolution 2.30&Aring;
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The line below this paragraph, containing "STRUCTURE_3b9x", creates the "Structure Box" on the page.
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|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Residue+A+400'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+B+400'>AC2</scene>, <scene name='pdbsite=AC3:Ca+Binding+Site+For+Residue+C+400'>AC3</scene>, <scene name='pdbsite=AC4:Ca+Binding+Site+For+Residue+D+400'>AC4</scene>, <scene name='pdbsite=AC5:Nos+Binding+Site+For+Residue+A+401'>AC5</scene>, <scene name='pdbsite=AC6:Nos+Binding+Site+For+Residue+B+401'>AC6</scene>, <scene name='pdbsite=AC7:Nos+Binding+Site+For+Residue+C+401'>AC7</scene>, <scene name='pdbsite=AC8:Nos+Binding+Site+For+Residue+D+401'>AC8</scene> and <scene name='pdbsite=AC9:Tam+Binding+Site+For+Residue+D+402'>AC9</scene>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NOS:INOSINE'>NOS</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </span>
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or leave the SCENE parameter empty for the default display.
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|GENE= rihB, yeiK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd02651 nuc_hydro_IU_UC_XIUA], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK10443 rihA]</span>
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{{STRUCTURE_3b9x| PDB=3b9x | SCENE= }}
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|RELATEDENTRY=[[1q8f|1Q8F]], [[2mas|2MAS]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9x OCA], [http://www.ebi.ac.uk/pdbsum/3b9x PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3b9x RCSB]</span>
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}}
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'''Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine'''
'''Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine'''
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[[Category: Hydrolase]]
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[[Category: hydrolase]]
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[[Category: Nh-fold]]
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[[Category: nh-fold]]
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[[Category: Protein-nucleoside complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:32:23 2008''
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[[Category: protein-nucleoside complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:59:10 2008''
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Revision as of 06:32, 24 April 2008

Image:3b9x.jpg

Template:STRUCTURE 3b9x

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine


Overview

Enzymes with nucleoside hydrolase activity (NHs) belonging to homology group I either are markedly specific for pyrimidine nucleoside substrates or hydrolyze with comparable efficiencies the N-glycosidic bond in all common nucleosides. The biochemical and structural basis for these differences in substrate specificity is still unknown. Here we characterize the binding interactions between the slowly hydrolyzed substrate inosine and the Escherichia coli pyrimidine-specific NH YeiK using cryotrapping and X-ray crystallography. Guided by the structural features of the Michaelis complex, we show the synergic effect of two specific point mutations in YeiK that increase the catalytic efficiency toward purine nucleosides to values comparable to those of natural nonspecific NHs. We demonstrate that the integrity of an active-site catalytic triad comprised of two hydroxylated amino acids and one histidine residue is a requirement for the highly efficient hydrolysis of inosine by group I NHs. Instead, cleavage of the YeiK-preferred substrate uridine is not affected by mutations at the same locations, suggesting a different fine chemical mechanism for the hydrolysis of the two nucleoside substrates. Our study provides for the first time direct evidence that distinct subsets of amino acid residues are involved in the hydrolysis of purine or pyrimidine nucleosides in group I NHs.

About this Structure

3B9X is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

Structural Basis for Substrate Specificity in Group I Nucleoside Hydrolases(,)., Iovane E, Giabbai B, Muzzolini L, Matafora V, Fornili A, Minici C, Giannese F, Degano M, Biochemistry. 2008 Mar 25;. PMID:18361502 Page seeded by OCA on Thu Apr 24 09:32:23 2008

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