3nl9
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3nl9 is ON HOLD Authors: Joint Center for Structural Genomics (JCSG) Description: Crystal structure of a putative NTP pyrophosphohydrolase (Exig_10...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of a putative NTP pyrophosphohydrolase (Exig_1061) from EXIGUOBACTERIUM SP. 255-15 at 1.78 A resolution== | |
| + | <StructureSection load='3nl9' size='340' side='right'caption='[[3nl9]], [[Resolution|resolution]] 1.78Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3nl9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Exiguobacterium_sibiricum_255-15 Exiguobacterium sibiricum 255-15]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3mqu 3mqu] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2rfp 2rfp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NL9 FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=3nl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nl9 OCA], [https://pdbe.org/3nl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nl9 RCSB], [https://www.ebi.ac.uk/pdbsum/3nl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nl9 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/B1YMF4_EXIS2 B1YMF4_EXIS2] | ||
| + | == 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/nl/3nl9_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/main_output.php?pdb_ID=3nl9 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 A resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-alpha-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other alpha-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity. | ||
| - | + | Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.,Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1237-44. Epub 2010 Aug 4. PMID:20944217<ref>PMID:20944217</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 3nl9" style="background-color:#fffaf0;"></div> | |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Exiguobacterium sibiricum 255-15]] | ||
| + | [[Category: Large Structures]] | ||
Current revision
Crystal structure of a putative NTP pyrophosphohydrolase (Exig_1061) from EXIGUOBACTERIUM SP. 255-15 at 1.78 A resolution
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