1su2
From Proteopedia
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==CRYSTAL STRUCTURE OF THE NUDIX HYDROLASE DR1025 IN COMPLEX WITH ATP== | ==CRYSTAL STRUCTURE OF THE NUDIX HYDROLASE DR1025 IN COMPLEX WITH ATP== | ||
| - | <StructureSection load='1su2' size='340' side='right' caption='[[1su2]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='1su2' size='340' side='right'caption='[[1su2]], [[Resolution|resolution]] 1.60Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1su2]] is a 2 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1su2]] is a 2 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=1SU2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SU2 FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1su2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1su2 OCA], [https://pdbe.org/1su2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1su2 RCSB], [https://www.ebi.ac.uk/pdbsum/1su2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1su2 ProSAT], [https://www.topsan.org/Proteins/BSGC/1su2 TOPSAN]</span></td></tr> |
</table> | </table> | ||
| + | == Function == | ||
| + | [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> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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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=1su2 ConSurf]. | </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=1su2 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | 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. | ||
| - | + | ==See Also== | |
| - | + | *[[Nudix hydrolase|Nudix hydrolase]] | |
| - | + | *[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]] | |
| - | + | *[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]] | |
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== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Deinococcus radiodurans]] |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Bessman | + | [[Category: Bessman MJ]] |
| - | [[Category: Brenner | + | [[Category: Brenner SE]] |
| - | [[Category: Hill | + | [[Category: Hill EE]] |
| - | [[Category: Holbrook | + | [[Category: Holbrook EL]] |
| - | [[Category: Holbrook | + | [[Category: Holbrook SR]] |
| - | [[Category: Mooster | + | [[Category: Mooster JL]] |
| - | [[Category: Ranatunga | + | [[Category: Ranatunga W]] |
| - | [[Category: Schulze-Gahmen | + | [[Category: Schulze-Gahmen U]] |
| - | [[Category: Xu | + | [[Category: Xu W]] |
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Current revision
CRYSTAL STRUCTURE OF THE NUDIX HYDROLASE DR1025 IN COMPLEX WITH ATP
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