2pan

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[[Image:2pan.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of E. coli glyoxylate carboligase==
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|PDB= 2pan |SIZE=350|CAPTION= <scene name='initialview01'>2pan</scene>, resolution 2.70&Aring;
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<StructureSection load='2pan' size='340' side='right'caption='[[2pan]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+A+851'>AC1</scene>, <scene name='pdbsite=AC2:Mg+Binding+Site+For+Residue+B+851'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Residue+C+851'>AC3</scene>, <scene name='pdbsite=AC4:Mg+Binding+Site+For+Residue+D+851'>AC4</scene>, <scene name='pdbsite=AC5:Mg+Binding+Site+For+Residue+E+851'>AC5</scene>, <scene name='pdbsite=AC6:Mg+Binding+Site+For+Residue+F+851'>AC6</scene>, <scene name='pdbsite=AC7:Mg+Binding+Site+For+Residue+A+1501'>AC7</scene>, <scene name='pdbsite=AC8:Mg+Binding+Site+For+Residue+B+1501'>AC8</scene>, <scene name='pdbsite=AC9:Mg+Binding+Site+For+Residue+E+1501'>AC9</scene>, <scene name='pdbsite=BC1:Mg+Binding+Site+For+Residue+F+1501'>BC1</scene>, <scene name='pdbsite=BC2:Fad+Binding+Site+For+Residue+A+701'>BC2</scene>, <scene name='pdbsite=BC3:Tdp+Binding+Site+For+Residue+A+801'>BC3</scene>, <scene name='pdbsite=BC4:Dtt+Binding+Site+For+Residue+A+901'>BC4</scene>, <scene name='pdbsite=BC5:Fad+Binding+Site+For+Residue+B+701'>BC5</scene>, <scene name='pdbsite=BC6:Tdp+Binding+Site+For+Residue+B+801'>BC6</scene>, <scene name='pdbsite=BC7:Dtt+Binding+Site+For+Residue+B+901'>BC7</scene>, <scene name='pdbsite=BC8:Fad+Binding+Site+For+Residue+C+701'>BC8</scene>, <scene name='pdbsite=BC9:Tdp+Binding+Site+For+Residue+C+801'>BC9</scene>, <scene name='pdbsite=CC1:Dtt+Binding+Site+For+Residue+C+901'>CC1</scene>, <scene name='pdbsite=CC2:Fad+Binding+Site+For+Residue+D+701'>CC2</scene>, <scene name='pdbsite=CC3:Tdp+Binding+Site+For+Residue+D+801'>CC3</scene>, <scene name='pdbsite=CC4:Dtt+Binding+Site+For+Residue+D+901'>CC4</scene>, <scene name='pdbsite=CC5:Fad+Binding+Site+For+Residue+E+701'>CC5</scene>, <scene name='pdbsite=CC6:Tdp+Binding+Site+For+Residue+E+801'>CC6</scene>, <scene name='pdbsite=CC7:Dtt+Binding+Site+For+Residue+E+901'>CC7</scene>, <scene name='pdbsite=CC8:Fad+Binding+Site+For+Residue+F+701'>CC8</scene>, <scene name='pdbsite=CC9:Tdp+Binding+Site+For+Residue+F+801'>CC9</scene>, <scene name='pdbsite=DC1:Dtt+Binding+Site+For+Residue+F+901'>DC1</scene> and <scene name='pdbsite=DC2:1pe+Binding+Site+For+Residue+A+951'>DC2</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene> and <scene name='pdbligand=1PE:PENTAETHYLENE GLYCOL'>1PE</scene>
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<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>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Tartronate-semialdehyde_synthase Tartronate-semialdehyde synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.47 4.1.1.47]
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</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>
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|GENE= gcl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<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>
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}}
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<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>
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<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>
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'''Crystal structure of E. coli glyoxylate carboligase'''
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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=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>
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</table>
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== Function ==
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==Overview==
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[[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).
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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/pa/2pan_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=2pan ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== 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.
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.
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==About this Structure==
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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>
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2PAN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PAN OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/18176558 18176558]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 2pan" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bacillus coli migula 1895]]
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[[Category: Large Structures]]
[[Category: Tartronate-semialdehyde synthase]]
[[Category: Tartronate-semialdehyde synthase]]
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[[Category: Barak, Z.]]
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[[Category: Barak, Z]]
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[[Category: Chipman, D M.]]
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[[Category: Chipman, D M]]
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[[Category: Kaplun, A.]]
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[[Category: Kaplun, A]]
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[[Category: Shaanan, B.]]
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[[Category: Shaanan, B]]
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[[Category: Vyazmensky, M.]]
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[[Category: Vyazmensky, M]]
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[[Category: 1PE]]
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[[Category: Enzyme]]
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[[Category: DTT]]
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[[Category: Fad]]
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[[Category: FAD]]
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[[Category: Glyoxylate carboligase]]
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[[Category: MG]]
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[[Category: Lyase]]
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[[Category: TDP]]
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[[Category: Thimain-dependent enzyme]]
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[[Category: enzyme]]
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[[Category: fad]]
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[[Category: glyoxylate carboligase]]
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[[Category: lyase]]
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[[Category: thiamin-diphosphate (thdp)]]
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[[Category: thimain-dependent enzyme]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:10:56 2008''
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Current revision

Crystal structure of E. coli glyoxylate carboligase

PDB ID 2pan

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