1k2e: Difference between revisions

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-[[Image:1k2e.jpg|left|200px]]
- {{Structure
+==crystal structure of a nudix protein from Pyrobaculum aerophilum==
-|PDB= 1k2e |SIZE=350|CAPTION= <scene name='initialview01'>1k2e</scene>, resolution 1.80&Aring;
+<StructureSection load='1k2e' size='340' side='right'caption='[[1k2e]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> and <scene name='pdbligand=ACY:ACETIC ACID'>ACY</scene>
+<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>
-|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]] 1.8&#8491;</td></tr>
-|GENE=
+<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.
-'''crystal structure of a nudix protein from Pyrobaculum aerophilum'''
+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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1k2e" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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.
+*[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-K2E 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=1K2E OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-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: 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: ACY]]
-[[Category: GOL]]
-[[Category: NI]]
-[[Category: SO4]]
-[[Category: dimer]]
-[[Category: mixed alpha/beta]]
-[[Category: nudix/mutt-like fold]]
-[[Category: putative nudix hydrolase]]
-[[Category: structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:11:38 2008''