3noj
From Proteopedia
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| - | [[ | + | ==The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida== |
| + | <StructureSection load='3noj' size='340' side='right' caption='[[3noj]], [[Resolution|resolution]] 1.82Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3noj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NOJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NOJ FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pput1361, Pput_1361 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-4-methyl-2-oxoglutarate_aldolase 4-hydroxy-4-methyl-2-oxoglutarate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.17 4.1.3.17] </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=3noj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3noj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3noj RCSB], [http://www.ebi.ac.uk/pdbsum/3noj PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | == 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/no/3noj_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/chain_selection.php?pdb_ID=2ata ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | HMG/CHA aldolase from Pseudomonas putida F1 catalyzes the last step of the bacterial protocatechuate 4,5- cleavage pathway. The enzyme's preferred substrates are 2-keto-4-hydroxy acids with a 4-carboxylate substitution. The enzyme also exhibits oxaloacetate decarboxylation and pyruvate alpha-proton exchange activity. Sodium oxalate is a competitive inhibitor of the aldolase reaction. The pH dependence of kcat/Km and kcat for the enzyme is consistent with a single deprotonation with pKa values of 8.0 +/- 0.1 and 7.0 +/- 0.1 for free enzyme and enzyme substrate complex, respectively. The 1.8 A x-ray structure shows a four-layered alpha-beta-beta-alpha sandwich structure with the active site at the interface of two adjacent subunits of a hexamer; this fold resembles the RNAse E inhibitor, RraA, but is novel for an aldolase. The catalytic site contains a magnesium ion ligated by Asp124 as well as three water molecules bound by Asp102 and Glu199. A pyruvate molecule binds the magnesium ion through both carboxylate and keto oxygen atoms, completing the octahedral geometry. The carbonyl oxygen also forms a hydrogen bonds with the guanadinium group of Arg123, which site-directed mutagenesis confirms is essential for catalysis. A mechanism for HMG/CHA aldolase is proposed on the basis of the structure, kinetics, and previously established features of other aldolase mechanisms. | ||
| - | + | Structural and kinetic characterization of 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy-4-hydroxy-2-oxoadipate (CHA) aldolase: a protocatechuate degradation enzyme evolutionarily convergent with the HpaI and DmpG pyruvate aldolases.,Wang W, Mazurkewich S, Kimber MS, Seah SY J Biol Chem. 2010 Sep 15. PMID:20843800<ref>PMID:20843800</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
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==See Also== | ==See Also== | ||
*[[Aldolase|Aldolase]] | *[[Aldolase|Aldolase]] | ||
| - | + | == References == | |
| - | == | + | <references/> |
| - | < | + | __TOC__ |
| + | </StructureSection> | ||
[[Category: 4-hydroxy-4-methyl-2-oxoglutarate aldolase]] | [[Category: 4-hydroxy-4-methyl-2-oxoglutarate aldolase]] | ||
[[Category: Pseudomonas putida]] | [[Category: Pseudomonas putida]] | ||
| - | [[Category: Kimber, M S | + | [[Category: Kimber, M S]] |
| - | [[Category: Mazurkewich, S | + | [[Category: Mazurkewich, S]] |
| - | [[Category: Seah, S Y.K | + | [[Category: Seah, S Y.K]] |
| - | [[Category: Wang, W | + | [[Category: Wang, W]] |
[[Category: A-b-b-a sandwich]] | [[Category: A-b-b-a sandwich]] | ||
[[Category: Class ii aldolase]] | [[Category: Class ii aldolase]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
[[Category: Metalloprotein]] | [[Category: Metalloprotein]] | ||
Revision as of 12:30, 9 December 2014
The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida
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