1k2e: Difference between revisions
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New page: left|200px<br /><applet load="1k2e" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k2e, resolution 1.80Å" /> '''crystal structure of... |
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== | ==crystal structure of a nudix protein from Pyrobaculum aerophilum== | ||
Nudix proteins, formerly called MutT homolog proteins, are a large family | <StructureSection load='1k2e' size='340' side='right'caption='[[1k2e]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1k2e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K2E FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1k2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k2e OCA], [https://pdbe.org/1k2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k2e RCSB], [https://www.ebi.ac.uk/pdbsum/1k2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k2e ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8ZTD8_PYRAE Q8ZTD8_PYRAE] | |||
== 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/k2/1k2e_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=1k2e ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nudix proteins, formerly called MutT homolog proteins, are a large family of proteins that play an important role in reducing the accumulation of potentially toxic compounds inside the cell. They hydrolyze a wide variety of substrates that are mainly composed of a nucleoside diphosphate linked to some other moiety X and thus are called Nudix hydrolases. Here, the crystal structure of a Nudix hydrolase from the hyperthermophilic archaeon Pyrobaculum aerophilum is reported. The structure was determined by the single-wavelength anomalous scattering method with data collected at the peak anomalous wavelength of an iridium-derivatized crystal. It reveals an extensive dimer interface, with each subunit contributing two strands to the beta-sheet of the other subunit. Individual subunits consist of a mixed highly twisted and curved beta-sheet of 11 beta-strands and two alpha-helices, forming an alpha-beta-alpha sandwich. The conserved Nudix box signature motif, which contains the essential catalytic residues, is located at the first alpha-helix and the beta-strand and loop preceding it. The unusually short connections between secondary-structural elements, together with the dimer form of the structure, are likely to contribute to the thermostability of the P. aerophilum Nudix protein. | |||
Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets.,Wang S, Mura C, Sawaya MR, Cascio D, Eisenberg D Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):571-8. Epub 2002, Mar 22. PMID:11914479<ref>PMID:11914479</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1k2e" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrobaculum aerophilum]] | [[Category: Pyrobaculum aerophilum]] | ||
[[Category: Cascio D]] | |||
[[Category: Cascio | [[Category: Eisenberg D]] | ||
[[Category: Eisenberg | [[Category: Mura C]] | ||
[[Category: Mura | [[Category: Sawaya MR]] | ||
[[Category: Sawaya | [[Category: Wang S]] | ||
[[Category: Wang | |||
Latest revision as of 08:49, 16 August 2023
crystal structure of a nudix protein from Pyrobaculum aerophilum
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