2q16

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[[Image:2q16.jpg|left|200px]]
[[Image:2q16.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 2q16 |SIZE=350|CAPTION= <scene name='initialview01'>2q16</scene>, resolution 1.95&Aring;
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The line below this paragraph, containing "STRUCTURE_2q16", creates the "Structure Box" on the page.
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|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Residue+A+200'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+B+200'>AC2</scene>, <scene name='pdbsite=AC3:Na+Binding+Site+For+Residue+A+201'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+B+201'>AC4</scene>, <scene name='pdbsite=AC5:Na+Binding+Site+For+Residue+B+202'>AC5</scene>, <scene name='pdbsite=AC6:Na+Binding+Site+For+Residue+A+202'>AC6</scene>, <scene name='pdbsite=AC7:Na+Binding+Site+For+Residue+A+203'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+A+6245'>AC8</scene>, <scene name='pdbsite=AC9:Itt+Binding+Site+For+Residue+A+6246'>AC9</scene> and <scene name='pdbsite=BC1:Itt+Binding+Site+For+Residue+B+203'>BC1</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=ITT:INOSINE+5&#39;-TRIPHOSPHATE'>ITT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </span>
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or leave the SCENE parameter empty for the default display.
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|GENE= yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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-->
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|DOMAIN=
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{{STRUCTURE_2q16| PDB=2q16 | SCENE= }}
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|RELATEDENTRY=[[1k7k|1K7K]], [[2pyu|2PYU]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q16 OCA], [http://www.ebi.ac.uk/pdbsum/2q16 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q16 RCSB]</span>
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}}
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'''Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP'''
'''Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP'''
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[[Category: Skarina, T.]]
[[Category: Skarina, T.]]
[[Category: Yakunin, A F.]]
[[Category: Yakunin, A F.]]
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[[Category: hydrolase]]
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[[Category: Hydrolase]]
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[[Category: itp pyrophosphatase x-ray structure enzyme mechanism substrate]]
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[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism substrate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 14:09:19 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:43:20 2008''
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Revision as of 11:09, 4 May 2008

Image:2q16.jpg

Template:STRUCTURE 2q16

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP


Overview

Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP+Ca(2+)) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha)-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases.

About this Structure

2Q16 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli., Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF, J Mol Biol. 2007 Dec 7;374(4):1091-103. Epub 2007 Oct 11. PMID:17976651 Page seeded by OCA on Sun May 4 14:09:19 2008

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