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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]] 1.60&Aring;' scene=''>
<StructureSection load='1su2' size='340' side='right'caption='[[1su2]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1su2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SU2 FirstGlance]. <br>
<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR1025 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>
<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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1su2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1su2 OCA], [http://pdbe.org/1su2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1su2 RCSB], [http://www.ebi.ac.uk/pdbsum/1su2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1su2 ProSAT], [http://www.topsan.org/Proteins/BSGC/1su2 TOPSAN]</span></td></tr>
<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.


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:15123424<ref>PMID:15123424</ref>
==See Also==
 
*[[Nudix hydrolase|Nudix hydrolase]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
*[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]]
</div>
*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
<div class="pdbe-citations 1su2" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Micrococcus radiodurans raj et al. 1960]]
[[Category: Deinococcus radiodurans]]
[[Category: Structural genomic]]
[[Category: Large Structures]]
[[Category: Bessman, M J]]
[[Category: Bessman MJ]]
[[Category: Brenner, S E]]
[[Category: Brenner SE]]
[[Category: Hill, E E]]
[[Category: Hill EE]]
[[Category: Holbrook, E L]]
[[Category: Holbrook EL]]
[[Category: Holbrook, S R]]
[[Category: Holbrook SR]]
[[Category: Mooster, J L]]
[[Category: Mooster JL]]
[[Category: Ranatunga, W]]
[[Category: Ranatunga W]]
[[Category: Schulze-Gahmen, U]]
[[Category: Schulze-Gahmen U]]
[[Category: Xu, W]]
[[Category: Xu W]]
[[Category: Alpha-beta-alpha sandwich]]
[[Category: Bsgc structure funded by nih]]
[[Category: Hydrolase]]
[[Category: Nudix fold]]
[[Category: PSI, Protein structure initiative]]

Latest revision as of 11:33, 14 February 2024

CRYSTAL STRUCTURE OF THE NUDIX HYDROLASE DR1025 IN COMPLEX WITH ATPCRYSTAL STRUCTURE OF THE NUDIX HYDROLASE DR1025 IN COMPLEX WITH ATP

Structural highlights

1su2 is a 2 chain structure with sequence from Deinococcus radiodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Xu A, Desai AM, Brenner SE, Kirsch JF. A continuous fluorescence assay for the characterization of Nudix hydrolases. Anal Biochem. 2013 Jun 15;437(2):178-84. PMID:23481913 doi:10.1016/j.ab.2013.02.023

1su2, resolution 1.60Å

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