2yvp

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[[Image:2yvp.jpg|left|200px]]
[[Image:2yvp.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 2yvp |SIZE=350|CAPTION= <scene name='initialview01'>2yvp</scene>, resolution 1.66&Aring;
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The line below this paragraph, containing "STRUCTURE_2yvp", creates the "Structure Box" on the page.
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|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+A+183'>AC1</scene>, <scene name='pdbsite=AC2:Mg+Binding+Site+For+Residue+A+184'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Residue+A+185'>AC3</scene> and <scene name='pdbsite=AC4:Rby+Binding+Site+For+Residue+A+186'>AC4</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RBY:METHYLENE+ADP-BETA-XYLOSE'>RBY</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=
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or leave the SCENE parameter empty for the default display.
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|GENE= ndx2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
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-->
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|DOMAIN=
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{{STRUCTURE_2yvp| PDB=2yvp | SCENE= }}
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|RELATEDENTRY=[[2yvm|2YVM]], [[2yvn|2YVN]], [[2yvo|2YVO]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvp OCA], [http://www.ebi.ac.uk/pdbsum/2yvp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2yvp RCSB]</span>
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}}
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'''Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8'''
'''Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8'''
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[[Category: Wakamatsu, T.]]
[[Category: Wakamatsu, T.]]
[[Category: Yokoyama, S.]]
[[Category: Yokoyama, S.]]
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[[Category: adp-ribose]]
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[[Category: Adp-ribose]]
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[[Category: fad]]
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[[Category: Fad]]
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[[Category: hydrolase]]
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[[Category: Hydrolase]]
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[[Category: national project on protein structural and functional analyse]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: nppsfa]]
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[[Category: Nppsfa]]
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[[Category: nudix protein]]
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[[Category: Nudix protein]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: Rsgi]]
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[[Category: structural genomic]]
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[[Category: Structural genomic]]
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[[Category: thermus thermophilus]]
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[[Category: Thermus thermophilus]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 19:32:42 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:15:53 2008''
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Revision as of 16:32, 4 May 2008

Image:2yvp.jpg

Template:STRUCTURE 2yvp

Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8


Overview

ADP-ribose (ADPR) is one of the main substrates of Nudix proteins. Among the eight Nudix proteins of Thermus thermophilus HB8, we previously determined the crystal structure of Ndx4, an ADPR pyrophosphatase (ADPRase). In this study we show that Ndx2 of T. thermophilus also preferentially hydrolyzes ADPR and flavin adenine dinucleotide and have determined its crystal structure. We have determined the structures of Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue. Although Ndx2 recognizes the AMP moiety in a manner similar to those for other ADPRases, it recognizes the terminal ribose in a distinct manner. The residues responsible for the recognition of the substrate in Ndx2 are not conserved among ADPRases. This may reflect the diversity in substrate specificity among ADPRases. Based on these results, we propose the classification of ADPRases into two types: ADPRase-I enzymes, which exhibit high specificity for ADPR; and ADPRase-II enzymes, which exhibit low specificity for ADPR. In the active site of the ternary complexes, three Mg2+ ions are coordinated to the side chains of conserved glutamate residues and water molecules. Substitution of Glu90 and Glu94 with glutamine suggests that these residues are essential for catalysis. These results suggest that ADPRase-I and ADPRase-II enzymes have nearly identical catalytic mechanisms but different mechanisms of substrate recognition.

About this Structure

2YVP is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.

Reference

Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8., Wakamatsu T, Nakagawa N, Kuramitsu S, Masui R, J Bacteriol. 2008 Feb;190(3):1108-17. Epub 2007 Nov 26. PMID:18039767 Page seeded by OCA on Sun May 4 19:32:42 2008

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