1soi

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[[Image:1soi.gif|left|200px]]<br /><applet load="1soi" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1soi, resolution 1.8&Aring;" />
 
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'''CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3==
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We have determined the crystal structure, at 1.4A, of the Nudix hydrolase DR1025 from the extremely radiation resistant bacterium Deinococcus radiodurans. The protein forms an intertwined homodimer by exchanging N-terminal segments between chains. We have identified additional conserved elements of the Nudix fold, including the metal-binding motif, a kinked beta-strand characterized by a proline two positions upstream of the Nudix consensus sequence, and participation of the N-terminal extension in the formation of the substrate-binding pocket. Crystal structures were also solved of DR1025 crystallized in the presence of magnesium and either a GTP analog or Ap(4)A (both at 1.6A resolution). In the Ap(4)A co-crystal, the electron density indicated that the product of asymmetric hydrolysis, ATP, was bound to the enzyme. The GTP analog bound structure showed that GTP was bound almost identically as ATP. Neither nucleoside triphosphate was further cleaved.
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<StructureSection load='1soi' size='340' side='right'caption='[[1soi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1soi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SOI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SOI FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1soi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1soi OCA], [https://pdbe.org/1soi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1soi RCSB], [https://www.ebi.ac.uk/pdbsum/1soi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1soi ProSAT], [https://www.topsan.org/Proteins/BSGC/1soi TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Y1025_DEIRA Y1025_DEIRA] Hydrolase that can act as a nucleoside triphosphatase and a dinucleoside polyphosphate pyrophosphatase. The best substrates are 8-oxo-dGTP and 8-oxo-GTP. Other substrates include Ap4A, dGTP and GTP. May be involved in protection from damage caused by radiation.<ref>PMID:23481913</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/so/1soi_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1soi ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1SOI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] with <scene name='pdbligand=SM:'>SM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SOI OCA].
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*[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]]
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== References ==
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==Reference==
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<references/>
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Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes., Ranatunga W, Hill EE, Mooster JL, Holbrook EL, Schulze-Gahmen U, Xu W, Bessman MJ, Brenner SE, Holbrook SR, J Mol Biol. 2004 May 21;339(1):103-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15123424 15123424]
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__TOC__
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</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: BSGC, Berkeley Structural Genomics Center.]]
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[[Category: Bessman MJ]]
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[[Category: Bessman, M J.]]
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[[Category: Brenner SE]]
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[[Category: Brenner, S E.]]
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[[Category: Hill EE]]
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[[Category: Hill, E E.]]
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[[Category: Holbrook EL]]
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[[Category: Holbrook, E L.]]
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[[Category: Holbrook SR]]
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[[Category: Holbrook, S R.]]
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[[Category: Mooster JL]]
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[[Category: Mooster, J L.]]
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[[Category: Ranatunga W]]
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[[Category: Ranatunga, W.]]
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[[Category: Schulze-Gahmen U]]
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[[Category: Schulze-Gahmen, U.]]
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[[Category: Xu W]]
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[[Category: Xu, W.]]
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[[Category: SM]]
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[[Category: alpha-beta-alpha sandwich]]
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[[Category: berkeley structural genomics center]]
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[[Category: bsgc structure funded by nih]]
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[[Category: nudix fold]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: structural genomics]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:03:39 2008''
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Current revision

CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3

PDB ID 1soi

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