1geq: Difference between revisions

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-[[Image:1geq.gif|left|200px]]
-<!--
+==Entropic stabilization of the tryptophan synthase A-subunit from a hyperthermophile, pyrococcus furiosus: X-ray analysis and calorimetry==
-The line below this paragraph, containing "STRUCTURE_1geq", creates the "Structure Box" on the page.
+<StructureSection load='1geq' size='340' side='right'caption='[[1geq]], [[Resolution|resolution]] 2.00&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'>[[1geq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GEQ 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&#8491;</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=1geq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1geq OCA], [https://pdbe.org/1geq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1geq RCSB], [https://www.ebi.ac.uk/pdbsum/1geq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1geq ProSAT]</span></td></tr>
-{{STRUCTURE_1geq|  PDB=1geq  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRPA_PYRFU TRPA_PYRFU] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.
+== 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/ge/1geq_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=1geq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the tryptophan synthase alpha-subunit from Pyrococcus furiosus was determined by x-ray analysis at 2.0-A resolution, and its stability was examined by differential scanning calorimetry. Although the structure of the tryptophan synthase alpha(2)beta(2) complex from Salmonella typhimurium has been already determined, this is the first report of the structure of the alpha-subunit alone. The alpha-subunit from P. furiosus (Pf-alpha-subunit) lacked 12 and 6 residues at the N and C termini, respectively, and one residue each in two loop regions as compared with that from S. typhimurium (St-alpha-subunit), resulting in the absence of an N-terminal helix and the shortening of a C-terminal helix. The structure of the Pf-alpha-subunit was essentially similar to that of the St-alpha-subunit in the alpha(2)beta(2) complex. The differences between both structures were discussed in connection with the higher stability of the Pf-alpha-subunit and the complex formation of the alpha- and beta-subunits. Calorimetric results indicated that the Pf-alpha-subunit has extremely high thermostability and that its higher stability is caused by an entropic effect. On the basis of structural information of both proteins, we analyzed the contributions of each stabilization factor and could conclude that hydrophobic interactions in the protein interior do not contribute to the higher stability of the Pf-alpha-subunit. Rather, the increase in ion pairs, decrease in cavity volume, and entropic effects due to shortening of the polypeptide chain play important roles in extremely high stability in Pf-alpha-subunit.
-'''ENTROPIC STABILIZATION OF THE TRYPTOPHAN SYNTHASE A-SUBUNIT FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS: X-RAY ANALYSIS AND CALORIMETRY'''
+Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry.,Yamagata Y, Ogasahara K, Hioki Y, Lee SJ, Nakagawa A, Nakamura H, Ishida M, Kuramitsu S, Yutani K J Biol Chem. 2001 Apr 6;276(14):11062-71. Epub 2000 Dec 15. PMID:11118452<ref>PMID:11118452</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1geq" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The structure of the tryptophan synthase alpha-subunit from Pyrococcus furiosus was determined by x-ray analysis at 2.0-A resolution, and its stability was examined by differential scanning calorimetry. Although the structure of the tryptophan synthase alpha(2)beta(2) complex from Salmonella typhimurium has been already determined, this is the first report of the structure of the alpha-subunit alone. The alpha-subunit from P. furiosus (Pf-alpha-subunit) lacked 12 and 6 residues at the N and C termini, respectively, and one residue each in two loop regions as compared with that from S. typhimurium (St-alpha-subunit), resulting in the absence of an N-terminal helix and the shortening of a C-terminal helix. The structure of the Pf-alpha-subunit was essentially similar to that of the St-alpha-subunit in the alpha(2)beta(2) complex. The differences between both structures were discussed in connection with the higher stability of the Pf-alpha-subunit and the complex formation of the alpha- and beta-subunits. Calorimetric results indicated that the Pf-alpha-subunit has extremely high thermostability and that its higher stability is caused by an entropic effect. On the basis of structural information of both proteins, we analyzed the contributions of each stabilization factor and could conclude that hydrophobic interactions in the protein interior do not contribute to the higher stability of the Pf-alpha-subunit. Rather, the increase in ion pairs, decrease in cavity volume, and entropic effects due to shortening of the polypeptide chain play important roles in extremely high stability in Pf-alpha-subunit.
+*[[Tryptophan synthase 3D structures|Tryptophan synthase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-GEQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GEQ OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry., Yamagata Y, Ogasahara K, Hioki Y, Lee SJ, Nakagawa A, Nakamura H, Ishida M, Kuramitsu S, Yutani K, J Biol Chem. 2001 Apr 6;276(14):11062-71. Epub 2000 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11118452 11118452]
-[[Category: Pyrococcus furiosus]]
-[[Category: Single protein]]
-[[Category: Yamagata, Y.]]
-[[Category: Yutani, K.]]
-[[Category: Calorimetry]]
-[[Category: Hyperthermophile]]
 [[Category: Pyrococcus furiosus]]
-[[Category: Stability]]
+[[Category: Yamagata Y]]
-[[Category: Tryptophan synthase alpha-subunit]]
+[[Category: Yutani K]]
-[[Category: X-ray analysis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 17:28:47 2008''