1jrk: Difference between revisions

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[[Image:1jrk.jpg|left|200px]]


{{Structure
==Crystal Structure of a Nudix Protein from Pyrobaculum aerophilum Reveals a Dimer with Intertwined Beta Sheets==
|PDB= 1jrk |SIZE=350|CAPTION= <scene name='initialview01'>1jrk</scene>, resolution 2.4&Aring;
<StructureSection load='1jrk' size='340' side='right'caption='[[1jrk]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
<table><tr><td colspan='2'>[[1jrk]] is a 4 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=1JRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JRK FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jrk OCA], [https://pdbe.org/1jrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jrk RCSB], [https://www.ebi.ac.uk/pdbsum/1jrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jrk ProSAT]</span></td></tr>
|RELATEDENTRY=[[1mut|1MUT]], [[1tum|1TUM]], [[1k2e|1K2E]], [[1k26|1K26]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jrk OCA], [http://www.ebi.ac.uk/pdbsum/1jrk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jrk RCSB]</span>
== 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/jr/1jrk_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=1jrk ConSurf].
<div style="clear:both"></div>


'''Crystal Structure of a Nudix Protein from Pyrobaculum aerophilum Reveals a Dimer with Intertwined Beta Sheets'''
==See Also==
 
*[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
==About this Structure==
1JRK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRK OCA].
 
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/11914479 11914479]
[[Category: Pyrobaculum aerophilum]]
[[Category: Pyrobaculum aerophilum]]
[[Category: Single protein]]
[[Category: Cascio D]]
[[Category: Cascio, D.]]
[[Category: Eisenberg D]]
[[Category: Eisenberg, D.]]
[[Category: Mura C]]
[[Category: Mura, C.]]
[[Category: Sawaya MR]]
[[Category: Sawaya, M R.]]
[[Category: Wang S]]
[[Category: Wang, S.]]
[[Category: mixed alpha/beta]]
[[Category: nudix/mutt-like fold]]
[[Category: putative nudix hydrolase]]
[[Category: structural genomic]]
[[Category: tetramerization due to hix6x tag]]
 
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