2yvk: Difference between revisions

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{{Seed}}
[[Image:2yvk.png|left|200px]]


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==Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis==
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<StructureSection load='2yvk' size='340' side='right'caption='[[2yvk]], [[Resolution|resolution]] 2.40&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'>[[2yvk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YVK 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]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MRU:5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE'>MRU</scene></td></tr>
{{STRUCTURE_2yvk|  PDB=2yvk  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvk OCA], [https://pdbe.org/2yvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yvk RCSB], [https://www.ebi.ac.uk/pdbsum/2yvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yvk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MTNA_BACSU MTNA_BACSU] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).<ref>PMID:14551435</ref>
== 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/yv/2yvk_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=2yvk ConSurf].
<div style="clear:both"></div>
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== Publication Abstract from PubMed ==
The methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report the crystal structures of B. subtilis M1Pi (Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate at 2.4 and 2.7 A resolution, respectively. The electron density clearly shows the presence of each compound in the active site. The structural comparison with other homologous proteins explains how the substrate uptake of Bs-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.


===Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis===
Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism.,Tamura H, Saito Y, Ashida H, Inoue T, Kai Y, Yokota A, Matsumura H Protein Sci. 2008 Jan;17(1):126-35. PMID:18156470<ref>PMID:18156470</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 18156470 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_18156470}}
__TOC__
 
</StructureSection>
==About this Structure==
2YVK is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVK OCA].
 
==Reference==
<ref group="xtra">PMID:18156470</ref><references group="xtra"/>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
[[Category: Large Structures]]
[[Category: Inoue, T.]]
[[Category: Inoue T]]
[[Category: Kai, Y.]]
[[Category: Kai Y]]
[[Category: Matsumura, H.]]
[[Category: Matsumura H]]
[[Category: Tamura, H.]]
[[Category: Tamura H]]
[[Category: Crystal structure]]
[[Category: Isomerase]]
[[Category: Methionine salvage pathway]]
 
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Retrieved from "https://proteopedia.org/2yvk"