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1trd

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(New page: 200px<br /><applet load="1trd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1trd, resolution 2.5&Aring;" /> '''THE INFLUENCE OF CRYS...)
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[[Image:1trd.jpg|left|200px]]<br /><applet load="1trd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1trd, resolution 2.5&Aring;" />
 
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'''THE INFLUENCE OF CRYSTAL PACKING ON CRYSTALLOGRAPHIC BINDING STUDIES: A NEW CRYSTAL FORM OF TRYPANOSOMAL TIM'''<br />
 
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==Overview==
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==THE INFLUENCE OF CRYSTAL PACKING ON CRYSTALLOGRAPHIC BINDING STUDIES: A NEW CRYSTAL FORM OF TRYPANOSOMAL TIM==
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The structure of trypanosomal triosephosphate isomerase (TIM) has been, solved at a resolution of 2.1A in a new crystal form grown at pH 8.8 from, PEG6000. In this new crystal form (space group C2, cell dimensions 94.8 A, 48.3 A, 131.0 A, 90.0 degrees, 100.3 degrees, 90.0 degrees), TIM is, present in a ligand-free state. The asymmetric unit consists of two TIM, subunits. Each of these subunits is part of a dimer which is sitting on a, crystallographic twofold axis, such that the crystal packing is formed, from two TIM dimers in two distinct environments. The two constituent, monomers of a given dimer are, therefore, crystallographically equivalent., In the ligand-free state of TIM in this crystal form, the two types of, dimer are very similar in structure, with the flexible loops in the "open", conformation. For one dimer (termed molecule-1), the flexible loop, (loop-6) is involved in crystal contacts. Crystals of this type have been, used in soaking experiments with 0.4 M ammonium sulphate (studied at 2.4 A, resolution), and with 40 microM phosphoglycolohydroxamate (studied at 2.5, A resolution). It is found that transfer to 0.4 M ammonium sulphate (equal, to 80 times the Ki of sulphate for TIM), gives rise to significant, sulphate binding at the active site of one dimer (termed molecule-2), and, less significant binding at the active site of the other. In neither dimer, does sulphate induce a "closed" conformation. In a mother liquor, containing 40 microM phosphoglycolohydroxamate (equal to 10 times the Ki, of phosphoglycolohydroxamate for TIM), an inhibitor molecule binds at the, active site of only that dimer of which the flexible loop is free from, crystal contacts (molecule-2). In this dimer, it induces a closed, conformation. These three structures are compared and discussed with, respect to the mode of binding of ligand in the active site as well as, with respect to the conformational changes resulting from ligand binding.
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<StructureSection load='1trd' size='340' side='right'caption='[[1trd]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1trd]] 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=1TRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TRD FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#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=PGH:PHOSPHOGLYCOLOHYDROXAMIC+ACID'>PGH</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1trd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trd OCA], [https://pdbe.org/1trd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1trd RCSB], [https://www.ebi.ac.uk/pdbsum/1trd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1trd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TPIS_TRYBB TPIS_TRYBB]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tr/1trd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1trd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1TRD 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] with PGH as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1TRD OCA].
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*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structures of the "open" and "closed" state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: implications for the reaction mechanism., Noble ME, Zeelen JP, Wierenga RK, Proteins. 1993 Aug;16(4):311-26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8356028 8356028]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Triose-phosphate isomerase]]
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[[Category: Trypanosoma brucei brucei]]
[[Category: Trypanosoma brucei brucei]]
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[[Category: Noble, M.E.M.]]
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[[Category: Noble MEM]]
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[[Category: Wierenga, R.K.]]
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[[Category: Wierenga RK]]
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[[Category: PGH]]
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[[Category: intramolecular oxidoreductase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:32:00 2007''
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Current revision

THE INFLUENCE OF CRYSTAL PACKING ON CRYSTALLOGRAPHIC BINDING STUDIES: A NEW CRYSTAL FORM OF TRYPANOSOMAL TIM

PDB ID 1trd

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