1wub: Difference between revisions

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<StructureSection load='1wub' size='340' side='right'caption='[[1wub]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
<StructureSection load='1wub' size='340' side='right'caption='[[1wub]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</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=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [https://pdbe.org/1wub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [https://www.ebi.ac.uk/pdbsum/1wub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wub ProSAT], [https://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></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=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [https://pdbe.org/1wub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [https://www.ebi.ac.uk/pdbsum/1wub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wub ProSAT], [https://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/P83815_THETH P83815_THETH]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1wub ConSurf].
</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=1wub ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. Here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, TT1927b, from Thermus thermophilus HB8, complexed with its ligand. This protein belongs to the YceI-like family in the Pfam database, and its sequence homologs are present in a broad range of bacteria and archaea. The structure consists of an extended, eight-stranded, antiparallel beta-barrel. In the hydrophobic pore of the barrel, the protein binds the polyisoprenoid chain by hydrophobic interactions. Its overall structure resembles the lipocalin fold, but there is no sequence homology between TT1927b and the lipocalin family of proteins.
Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8.,Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S Protein Sci. 2005 Apr;14(4):1004-10. Epub 2005 Mar 1. PMID:15741337<ref>PMID:15741337</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1wub" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Doi-Katayama, Y]]
[[Category: Thermus thermophilus]]
[[Category: Hamana, H]]
[[Category: Doi-Katayama Y]]
[[Category: Handa, N]]
[[Category: Hamana H]]
[[Category: Hirota, H]]
[[Category: Handa N]]
[[Category: Idaka, M]]
[[Category: Hirota H]]
[[Category: Ishizuka, Y]]
[[Category: Idaka M]]
[[Category: Kuramitsu, S]]
[[Category: Ishizuka Y]]
[[Category: Park, S Y]]
[[Category: Kuramitsu S]]
[[Category: Structural genomic]]
[[Category: Park S-Y]]
[[Category: Shirouzu, M]]
[[Category: Shirouzu M]]
[[Category: Tame, J R.H]]
[[Category: Tame JRH]]
[[Category: Terada, T]]
[[Category: Terada T]]
[[Category: Yokoyama, S]]
[[Category: Yokoyama S]]
[[Category: Beta-barrel]]
[[Category: Lipid binding protein]]
[[Category: Rsgi]]
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