3tim: Difference between revisions

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New page: left|200px<br /><applet load="3tim" size="450" color="white" frame="true" align="right" spinBox="true" caption="3tim, resolution 2.8Å" /> '''THE CRYSTAL STRUCTURE...
 
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[[Image:3tim.jpg|left|200px]]<br /><applet load="3tim" size="450" color="white" frame="true" align="right" spinBox="true"
caption="3tim, resolution 2.8&Aring;" />
'''THE CRYSTAL STRUCTURE OF THE "OPEN" AND THE "CLOSED" CONFORMATION OF THE FLEXIBLE LOOP OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE'''<br />


==Overview==
==THE CRYSTAL STRUCTURE OF THE "OPEN" AND THE "CLOSED" CONFORMATION OF THE FLEXIBLE LOOP OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE==
Triosephosphate isomerase has an important loop near the active site which, can exist in a "closed" and in an "open" conformation. Here we describe, the structural properties of this "flexible" loop observed in two, different structures of trypanosomal triosephosphate isomerase., Trypanosomal triosephosphate isomerase, crystallized in the presence of, 2.4 M ammonium sulfate, packs as an asymmetric dimer of 54,000 Da in the, crystallographic asymmetric unit. Due to different crystal contacts, peptide 167-180 (the flexible loop of subunit-1) is an open conformation, whereas in subunit-2, this peptide (residues 467-480) is in a closed, conformation. In the closed conformation, a hydrogen bond exists between, the tip of the loop and a well-defined sulfate ion which is bound to the, active site of subunit-2. Such an active site sulfate is not present in, subunit-1 due to crystal contacts. When the native (2.4 M ammonium, sulfate) crystals are transferred to a sulfate-free mother liquor, the, flexible loop of subunit-2 adopts the open conformation. From a closed, starting model, this open conformation was discovered through molecular, dynamics refinement without manual intervention, despite involving C alpha, shifts of up to 7 A. The tip of the loop, residues 472, 473, 474, and 475, moves as a rigid body. Our analysis shows that in this crystal form the, flexible loop of subunit-2 faces a solvent channel. Therefore the open and, the closed conformations of this flexible loop are virtually unaffected by, crystal contacts. The actual observed conformation depends only on the, absence or presence of a suitable ligand in the active site.
<StructureSection load='3tim' size='340' side='right'caption='[[3tim]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3tim]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TIM 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]] 2.8&#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=3tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tim OCA], [https://pdbe.org/3tim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tim RCSB], [https://www.ebi.ac.uk/pdbsum/3tim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tim ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TPIS_TRYBB TPIS_TRYBB]
== 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/ti/3tim_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=3tim ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
3TIM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Active as [http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3TIM OCA].
*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
The crystal structure of the "open" and the "closed" conformation of the flexible loop of trypanosomal triosephosphate isomerase., Wierenga RK, Noble ME, Postma JP, Groendijk H, Kalk KH, Hol WG, Opperdoes FR, Proteins. 1991;10(1):33-49. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2062827 2062827]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Triose-phosphate isomerase]]
[[Category: Trypanosoma brucei brucei]]
[[Category: Trypanosoma brucei brucei]]
[[Category: Wierenga, R.K.]]
[[Category: Wierenga RK]]
[[Category: isomerase(intramolecular oxidoreductse)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:59:41 2007''

Latest revision as of 13:09, 1 March 2024

THE CRYSTAL STRUCTURE OF THE "OPEN" AND THE "CLOSED" CONFORMATION OF THE FLEXIBLE LOOP OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASETHE CRYSTAL STRUCTURE OF THE "OPEN" AND THE "CLOSED" CONFORMATION OF THE FLEXIBLE LOOP OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE

Structural highlights

3tim is a 2 chain structure with sequence from Trypanosoma brucei brucei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TPIS_TRYBB

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

3tim, resolution 2.80Å

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