1lyx: Difference between revisions

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==Plasmodium Falciparum Triosephosphate Isomerase (PfTIM)-Phosphoglycolate complex==
==Plasmodium Falciparum Triosephosphate Isomerase (PfTIM)-Phosphoglycolate complex==
<StructureSection load='1lyx' size='340' side='right' caption='[[1lyx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='1lyx' size='340' side='right'caption='[[1lyx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1lyx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plafa Plafa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LYX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LYX FirstGlance]. <br>
<table><tr><td colspan='2'>[[1lyx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LYX FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lzo|1lzo]], [[1ydv|1ydv]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TPI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5833 PLAFA])</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=1lyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lyx OCA], [https://pdbe.org/1lyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lyx RCSB], [https://www.ebi.ac.uk/pdbsum/1lyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lyx ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lyx OCA], [http://pdbe.org/1lyx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lyx RCSB], [http://www.ebi.ac.uk/pdbsum/1lyx PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TPIS_PLAFA TPIS_PLAFA]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ly/1lyx_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ly/1lyx_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 19: Line 20:
</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=1lyx ConSurf].
</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=1lyx ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Triosephosphate isomerase (TIM) has been the subject of many structural and mechanistic studies. At position 96, there is a highly conserved Ser residue, which is proximal to the catalytic site. Thus far, no specific role has been ascribed to this residue. Plasmodium falciparum TIM (PfTIM), a fully catalytically active enzyme, is unique in possessing a Phe residue at position 96. The structure of PfTIM complexed to phosphoglycolate (PG), a transition state analogue, has been determined in an effort to probe the effects of the mutation at residue 96 on the nature of inhibitor-enzyme interactions and the orientation of the critical catalytic loop (loop 6, residues 166-176) in TIM. Crystal structures of PfTIM complexed to phosphoglycolate in orthorhombic (P2(1)2(1)2(1)) and monoclinic (C2) forms were determined and refined at resolutions of 2.8 and 1.9 A, respectively. The P2(1)2(1)2(1) form contains two dimers in the asymmetric unit. In the C2 form, the molecular and crystal 2-fold axes are coincident, leading to a monomer in the asymmetric unit. The catalytic loop adopts the open state in the P2(1)2(1)2(1) form and the closed conformation in the C2 crystal. The open conformation of the loop in the P2(1)2(1)2(1) form appears to be a consequence of the Ser to Phe mutation at residue 96. The steric clash between Phe96 and Ile172 probably impedes loop closure in PfTIM-ligand complexes. The PfTIM-PG complex is the first example of a TIM-ligand complex being observed in both loop open and closed forms. In the C2 form (loop closed), Phe96 and Leu167 adopt alternative conformations that are different from the ones observed in the open form, permitting loop closure. These structures provide strong support for the view that loop closure is not essential for ligand binding and that dynamic loop movement may occur in both free and ligand-bound forms of the enzyme.
Structure of the Plasmodium falciparum triosephosphate isomerase-phosphoglycolate complex in two crystal forms: characterization of catalytic loop open and closed conformations in the ligand-bound state.,Parthasarathy S, Ravindra G, Balaram H, Balaram P, Murthy MR Biochemistry. 2002 Nov 5;41(44):13178-88. PMID:12403619<ref>PMID:12403619</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1lyx" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Triose Phosphate Isomerase|Triose Phosphate Isomerase]]
*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Plafa]]
[[Category: Large Structures]]
[[Category: Triose-phosphate isomerase]]
[[Category: Plasmodium falciparum]]
[[Category: Balaram, H]]
[[Category: Balaram H]]
[[Category: Balaram, P]]
[[Category: Balaram P]]
[[Category: Murthy, M R]]
[[Category: Murthy MR]]
[[Category: Parthasarathy, S]]
[[Category: Parthasarathy S]]
[[Category: Beta-alpha barrel]]
[[Category: Isomerase]]
[[Category: Tim barrel]]

Latest revision as of 10:37, 14 February 2024

Plasmodium Falciparum Triosephosphate Isomerase (PfTIM)-Phosphoglycolate complexPlasmodium Falciparum Triosephosphate Isomerase (PfTIM)-Phosphoglycolate complex

Structural highlights

1lyx is a 1 chain structure with sequence from Plasmodium falciparum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TPIS_PLAFA

Evolutionary Conservation

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

See Also

1lyx, resolution 1.90Å

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