1v8z: Difference between revisions
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< | ==X-ray crystal structure of the Tryptophan Synthase b2 Subunit from Hyperthermophile, Pyrococcus furiosus== | ||
<StructureSection load='1v8z' size='340' side='right'caption='[[1v8z]], [[Resolution|resolution]] 2.21Å' scene=''> | |||
You may | == Structural highlights == | ||
or | <table><tr><td colspan='2'>[[1v8z]] is a 4 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=1V8Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V8Z FirstGlance]. <br> | ||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.21Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=1v8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8z OCA], [https://pdbe.org/1v8z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v8z RCSB], [https://www.ebi.ac.uk/pdbsum/1v8z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8z ProSAT], [https://www.topsan.org/Proteins/RSGI/1v8z TOPSAN]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/TRPB1_PYRFU TRPB1_PYRFU] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine (By similarity). | |||
== 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/v8/1v8z_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=1v8z ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The structure of the tryptophan synthase beta2 subunit (Pfbeta2) from the hyperthermophile, Pyrococcus furiosus, was determined by X-ray crystallographic analysis at 2.2 A resolution, and its stability was examined by DSC. This is the first report of the X-ray structure of the tryptophan synthase beta2 subunit alone, although the structure of the tryptophan synthase alpha2beta2 complex from Salmonella typhimurium has already been reported. The structure of Pfbeta2 was essentially similar to that of the beta2 subunit (Stbeta2) in the alpha2beta2 complex from S. typhimurium. The sequence alignment with secondary structures of Pfbeta and Stbeta in monomeric form showed that six residues in the N-terminal region and three residues in the C-terminal region were deleted in Pfbeta, and one residue at Pro366 of Stbeta and at Ile63 of Pfbeta was inserted. The denaturation temperature of Pfbeta2 was higher by 35 degrees C than the reported values from mesophiles at approximately pH 8. On the basis of structural information on both proteins, the analyses of the contributions of each stabilization factor indicate that: (a) the higher stability of Pfbeta2 is not caused by either a hydrophobic interaction or an increase in ion pairs; (b) the number of hydrogen bonds involved in the main chains of Pfbeta is greater by about 10% than that of Stbeta, indicating that the secondary structures of Pfbeta are more stabilized than those of Stbeta and (c) the sequence of Pfbeta seems to be better fitted to an ideally stable structure than that of Stbeta, as assessed from X-ray structure data. | |||
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.,Hioki Y, Ogasahara K, Lee SJ, Ma J, Ishida M, Yamagata Y, Matsuura Y, Ota M, Ikeguchi M, Kuramitsu S, Yutani K Eur J Biochem. 2004 Jul;271(13):2624-35. PMID:15206928<ref>PMID:15206928</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1v8z" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Tryptophan synthase 3D structures|Tryptophan synthase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
[[Category: Pyrococcus furiosus]] | [[Category: Pyrococcus furiosus]] | ||
[[Category: Hioki Y]] | |||
[[Category: Ishida M]] | |||
[[Category: Hioki | [[Category: Kuramitsu S]] | ||
[[Category: Ishida | [[Category: Lee SJ]] | ||
[[Category: Kuramitsu | [[Category: Ma J]] | ||
[[Category: Lee | [[Category: Matsuura Y]] | ||
[[Category: Ma | [[Category: Ogasahara K]] | ||
[[Category: Matsuura | [[Category: Ota M]] | ||
[[Category: Ogasahara | [[Category: Yamagata Y]] | ||
[[Category: Ota | [[Category: Yutani K]] | ||
[[Category: Yamagata | |||
[[Category: Yutani | |||
Latest revision as of 10:50, 25 October 2023
X-ray crystal structure of the Tryptophan Synthase b2 Subunit from Hyperthermophile, Pyrococcus furiosusX-ray crystal structure of the Tryptophan Synthase b2 Subunit from Hyperthermophile, Pyrococcus furiosus
Structural highlights
FunctionTRPB1_PYRFU The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine (By similarity). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe structure of the tryptophan synthase beta2 subunit (Pfbeta2) from the hyperthermophile, Pyrococcus furiosus, was determined by X-ray crystallographic analysis at 2.2 A resolution, and its stability was examined by DSC. This is the first report of the X-ray structure of the tryptophan synthase beta2 subunit alone, although the structure of the tryptophan synthase alpha2beta2 complex from Salmonella typhimurium has already been reported. The structure of Pfbeta2 was essentially similar to that of the beta2 subunit (Stbeta2) in the alpha2beta2 complex from S. typhimurium. The sequence alignment with secondary structures of Pfbeta and Stbeta in monomeric form showed that six residues in the N-terminal region and three residues in the C-terminal region were deleted in Pfbeta, and one residue at Pro366 of Stbeta and at Ile63 of Pfbeta was inserted. The denaturation temperature of Pfbeta2 was higher by 35 degrees C than the reported values from mesophiles at approximately pH 8. On the basis of structural information on both proteins, the analyses of the contributions of each stabilization factor indicate that: (a) the higher stability of Pfbeta2 is not caused by either a hydrophobic interaction or an increase in ion pairs; (b) the number of hydrogen bonds involved in the main chains of Pfbeta is greater by about 10% than that of Stbeta, indicating that the secondary structures of Pfbeta are more stabilized than those of Stbeta and (c) the sequence of Pfbeta seems to be better fitted to an ideally stable structure than that of Stbeta, as assessed from X-ray structure data. The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.,Hioki Y, Ogasahara K, Lee SJ, Ma J, Ishida M, Yamagata Y, Matsuura Y, Ota M, Ikeguchi M, Kuramitsu S, Yutani K Eur J Biochem. 2004 Jul;271(13):2624-35. PMID:15206928[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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