1v4k: Difference between revisions

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-{{Seed}}
-[[Image:1v4k.png|left|200px]]
-<!--
+==Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima S77F mutant==
-The line below this paragraph, containing "STRUCTURE_1v4k", creates the "Structure Box" on the page.
+<StructureSection load='1v4k' size='340' side='right'caption='[[1v4k]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1v4k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V4K FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1v4k|  PDB=1v4k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v4k OCA], [https://pdbe.org/1v4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v4k RCSB], [https://www.ebi.ac.uk/pdbsum/1v4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v4k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9X1M1_THEMA Q9X1M1_THEMA]
+== 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/v4/1v4k_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=1v4k ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with isopentenyl pyrophosphate (IPP) to generate C40 octaprenyl pyrophosphate (OPP), which constitutes the side chain of bacterial ubiquinone or menaquinone. In this study, the first structure of long chain C40-OPPs from Thermotoga maritima has been determined to 2.28-A resolution. OPPs is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity. An elongated hydrophobic tunnel between D and F alpha-helices contains two DDXXD motifs on the top for substrate binding and is occupied at the bottom with two large residues Phe-52 and Phe-132. The products of the mutant F132A OPPs are predominantly C50, longer than the C40 synthesized by the wild-type and F52A mutant OPPs, suggesting that Phe-132 is the key residue for determining the product chain length. Ala-76 and Ser-77 located close to the FPP binding site and Val-73 positioned further down the tunnel were individually mutated to larger amino acids. A76Y and S77F mainly produce C20 indicating that the mutated large residues in the vicinity of the FPP site limit the substrate chain elongation. Ala-76 is the fifth amino acid upstream from the first DDXXD motif on helix D of OPPs, and its corresponding amino acid in FPPs is Tyr. In contrast, V73Y mutation led to additional accumulation of C30 intermediate. The new structure of the trans-type OPPs, together with the recently determined cis-type UPPs, significantly extends our understanding on the biosynthesis of long chain polyprenyl molecules.
-===Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima S77F mutant===
+Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic Thermotoga maritima and mechanism of product chain length determination.,Guo RT, Kuo CJ, Chou CC, Ko TP, Shr HL, Liang PH, Wang AH J Biol Chem. 2004 Feb 6;279(6):4903-12. Epub 2003 Nov 15. PMID:14617622<ref>PMID:14617622</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_14617622}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1v4k" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 14617622 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14617622}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-V4K is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V4K OCA].
-==Reference==
-Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic Thermotoga maritima and mechanism of product chain length determination., Guo RT, Kuo CJ, Chou CC, Ko TP, Shr HL, Liang PH, Wang AH, J Biol Chem. 2004 Feb 6;279(6):4903-12. Epub 2003 Nov 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14617622 14617622]
-[[Category: Single protein]]
 [[Category: Thermotoga maritima]]
-[[Category: Trans-octaprenyltranstransferase]]
+[[Category: Chou CC]]
-[[Category: Chou, C C.]]
+[[Category: Guo RT]]
-[[Category: Guo, R T.]]
+[[Category: Ko TP]]
-[[Category: Ko, T P.]]
+[[Category: Kuo CJ]]
-[[Category: Kuo, C J.]]
+[[Category: Liang PH]]
-[[Category: Liang, P H.]]
+[[Category: Shr HL]]
-[[Category: Shr, H L.]]
+[[Category: Wang AH-J]]
-[[Category: Wang, A H.J.]]
-[[Category: Thermophilic]]
-[[Category: Trans-type prenyltransferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 06:08:00 2008''