1wub

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1wub" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wub, resolution 1.65&Aring;" /> '''Crystal structure of...)
Current revision (13:34, 13 March 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1wub.jpg|left|200px]]<br /><applet load="1wub" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1wub, resolution 1.65&Aring;" />
 
-
'''Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8'''<br />
 
-
==Overview==
+
==Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8==
-
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.
+
<StructureSection load='1wub' size='340' side='right'caption='[[1wub]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<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>
-
1WUB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with OTP as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1UF6. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA].
+
</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>
-
==Reference==
+
<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>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15741337 15741337]
+
</table>
-
[[Category: Single protein]]
+
== Function ==
 +
[https://www.uniprot.org/uniprot/P83815_THETH P83815_THETH]
 +
== 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/wu/1wub_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=1wub ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
-
[[Category: Doi-Katayama, Y.]]
+
[[Category: Doi-Katayama Y]]
-
[[Category: Hamana, H.]]
+
[[Category: Hamana H]]
-
[[Category: Handa, N.]]
+
[[Category: Handa N]]
-
[[Category: Hirota, H.]]
+
[[Category: Hirota H]]
-
[[Category: Idaka, M.]]
+
[[Category: Idaka M]]
-
[[Category: Ishizuka, Y.]]
+
[[Category: Ishizuka Y]]
-
[[Category: Kuramitsu, S.]]
+
[[Category: Kuramitsu S]]
-
[[Category: Park, S.Y.]]
+
[[Category: Park S-Y]]
-
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+
[[Category: Shirouzu M]]
-
[[Category: Shirouzu, M.]]
+
[[Category: Tame JRH]]
-
[[Category: Tame, J.R.H.]]
+
[[Category: Terada T]]
-
[[Category: Terada, T.]]
+
[[Category: Yokoyama S]]
-
[[Category: Yokoyama, S.]]
+
-
[[Category: OTP]]
+
-
[[Category: beta-barrel]]
+
-
[[Category: riken structural genomics/proteomics initiative]]
+
-
[[Category: rsgi]]
+
-
[[Category: structural genomics]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:45:07 2007''
+

Current revision

Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8

PDB ID 1wub

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1wub"
Personal tools