2pan: Difference between revisions
New page: left|200px<br /><applet load="2pan" size="350" color="white" frame="true" align="right" spinBox="true" caption="2pan, resolution 2.70Å" /> '''Crystal structure of... |
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== | ==Crystal structure of E. coli glyoxylate carboligase== | ||
<StructureSection load='2pan' size='340' side='right'caption='[[2pan]], [[Resolution|resolution]] 2.70Å' scene=''> | |||
[[Category: | == Structural highlights == | ||
[[Category: | <table><tr><td colspan='2'>[[2pan]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PAN FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gcl ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tartronate-semialdehyde_synthase Tartronate-semialdehyde synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.47 4.1.1.47] </span></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=2pan FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pan OCA], [https://pdbe.org/2pan PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pan RCSB], [https://www.ebi.ac.uk/pdbsum/2pan PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pan ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/GCL_ECOLI GCL_ECOLI]] Catalyzes the condensation of two molecules of glyoxylate to give 2-hydroxy-3-oxopropanoate (also termed tartronate semialdehyde). | |||
== 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/pa/2pan_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=2pan ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Thiamine diphosphate (ThDP), a derivative of vitamin B1, is an enzymatic cofactor whose special chemical properties allow it to play critical mechanistic roles in a number of essential metabolic enzymes. It has been assumed that all ThDP-dependent enzymes exploit a polar interaction between a strictly conserved glutamate and the N1' of the ThDP moiety. The crystal structure of glyoxylate carboligase challenges this paradigm by revealing that valine replaces the conserved glutamate. Through kinetic, spectroscopic and site-directed mutagenesis studies, we show that although this extreme change lowers the rate of the initial step of the enzymatic reaction, it ensures efficient progress through subsequent steps. Glyoxylate carboligase thus provides a unique illustration of the fine tuning between catalytic stages imposed during evolution on enzymes catalyzing multistep processes. | |||
Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-dependent enzymes.,Kaplun A, Binshtein E, Vyazmensky M, Steinmetz A, Barak Z, Chipman DM, Tittmann K, Shaanan B Nat Chem Biol. 2008 Feb;4(2):113-8. Epub 2008 Jan 6. PMID:18176558<ref>PMID:18176558</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2pan" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus coli migula 1895]] | |||
[[Category: Large Structures]] | |||
[[Category: Tartronate-semialdehyde synthase]] | [[Category: Tartronate-semialdehyde synthase]] | ||
[[Category: Barak, Z | [[Category: Barak, Z]] | ||
[[Category: Chipman, D | [[Category: Chipman, D M]] | ||
[[Category: Kaplun, A | [[Category: Kaplun, A]] | ||
[[Category: Shaanan, B | [[Category: Shaanan, B]] | ||
[[Category: Vyazmensky, M | [[Category: Vyazmensky, M]] | ||
[[Category: | [[Category: Enzyme]] | ||
[[Category: | [[Category: Fad]] | ||
[[Category: | [[Category: Glyoxylate carboligase]] | ||
[[Category: Lyase]] | |||
[[Category: Thimain-dependent enzyme]] | |||
[[Category: | |||
[[Category: | |||
