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1q27

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

Structural highlights

1q27 is a 1 chain structure with sequence from Deinococcus radiodurans. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2]

Evolutionary Conservation

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

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Buchko GW, Ni S, Holbrook SR, Kennedy MA. Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium. Proteins. 2004 Jul 1;56(1):28-39. PMID:15162484 doi:10.1002/prot.20082
↑ Buchko GW, Litvinova O, Robinson H, Yakunin AF, Kennedy MA. Functional and Structural Characterization of DR_0079 from Deinococcus radiodurans, a Novel Nudix Hydrolase with a Preference for Cytosine (Deoxy)ribonucleoside 5'-Di- and Triphosphates. Biochemistry. 2008 May 31;. PMID:18512963 doi:http://dx.doi.org/10.1021/bi800099d
↑ Buchko GW, Ni S, Holbrook SR, Kennedy MA. Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium. Proteins. 2004 Jul 1;56(1):28-39. PMID:15162484 doi:10.1002/prot.20082

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1q27"

@@ Line 1: / Line 1: @@
 ==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 ==
-<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/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 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://pdbe.org/1q27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 PDBsum]</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>
 == Function ==
-[[http://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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q2/1q27_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q2/1q27_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata 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].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Micrococcus radiodurans raj et al. 1960]]
+[[Category: Deinococcus radiodurans]]
-[[Category: Buchko, G W]]
+[[Category: Large Structures]]
-[[Category: Holbrook, S R]]
+[[Category: Buchko GW]]
-[[Category: Kennedy, M A]]
+[[Category: Holbrook SR]]
-[[Category: Ni, S]]
+[[Category: Kennedy MA]]
-[[Category: Hydrolase]]
+[[Category: Ni S]]
-[[Category: Nudix hydrolase]]
-[[Category: Radiation resistance]]

1q27

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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