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==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==
==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==
<StructureSection load='1q27' size='340' side='right'caption='[[1q27]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
<StructureSection load='1q27' size='340' side='right'caption='[[1q27]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR0079 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [https://pdbe.org/1q27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [https://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 ProSAT]</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [https://pdbe.org/1q27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [https://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/Y079_DEIRA Y079_DEIRA]] Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.<ref>PMID:15162484</ref> <ref>PMID:18512963</ref>
[https://www.uniprot.org/uniprot/Y079_DEIRA Y079_DEIRA] Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.<ref>PMID:15162484</ref> <ref>PMID:18512963</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=1q27 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=1q27 ConSurf].
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== Publication Abstract from PubMed ==
Using nuclear magnetic resonance (NMR) based methods, including residual dipolar coupling restraints, we have determined the solution structure of the hypothetical Deinococcus radiodurans Nudix protein DR0079 (171 residues, MW = 19.3 kDa). The protein contains eight beta-strands and three alpha-helices organized into three subdomains: an N-terminal beta-sheet (1-34), a central Nudix core (35-140), and a C-terminal helix-turn-helix (141-171). The Nudix core and the C-terminal helix-turn-helix form the fundamental fold common to the Nudix family, a large mixed beta-sheet sandwiched between alpha-helices. The residues that compose the signature Nudix sequence, GX5EX7REUXEEXGU (where U = I, L, or V and X = any amino acid), are contained in a turn-helix-turn motif on the face of the mixed beta-sheet. Chemical shift mapping experiments suggest that DR0079 binds Mg2+. Experiments designed to determine the biological function of the protein indicate that it is not a type I isopentenyl-diphosphate delta-isomerase and that it does not bind alpha,beta-methyleneadenosine 5'-triphosphate (AMPCPP) or guanosine 5'-[beta,gamma-imido]triphosphate (GMPPNP). In this article, the structure of DR0079 is compared to other known Nudix protein structures, a potential substrate-binding surface is proposed, and its possible biological function is discussed.
Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium.,Buchko GW, Ni S, Holbrook SR, Kennedy MA Proteins. 2004 Jul 1;56(1):28-39. PMID:15162484<ref>PMID:15162484</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1q27" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Micrococcus radiodurans raj et al. 1960]]
[[Category: Deinococcus radiodurans]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Buchko, G W]]
[[Category: Buchko GW]]
[[Category: Holbrook, S R]]
[[Category: Holbrook SR]]
[[Category: Kennedy, M A]]
[[Category: Kennedy MA]]
[[Category: Ni, S]]
[[Category: Ni S]]
[[Category: Hydrolase]]
[[Category: Nudix hydrolase]]
[[Category: Radiation resistance]]

Revision as of 06:00, 17 April 2024

NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans

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