3noj

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{{Seed}}
 
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[[Image:3noj.png|left|200px]]
 
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==The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida==
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The line below this paragraph, containing "STRUCTURE_3noj", creates the "Structure Box" on the page.
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<StructureSection load='3noj' size='340' side='right'caption='[[3noj]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3noj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida_F1 Pseudomonas putida F1]. 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 [https://proteopedia.org/fgij/fg.htm?mol=3NOJ 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]] 1.82&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
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{{STRUCTURE_3noj| PDB=3noj | SCENE= }}
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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=3noj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3noj OCA], [https://pdbe.org/3noj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3noj RCSB], [https://www.ebi.ac.uk/pdbsum/3noj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3noj ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/HMGA_PSEP1 HMGA_PSEP1] Catalyzes the last step of the bacterial protocatechuate 4,5-cleavage pathway. The preferred substrates of the enzyme are 2-keto-4-hydroxy acids with a 4-carboxylate substitution. Catalyzes the conversion of 4-hydroxy-4-methyl-2-oxoglutarate (HMG) to pyruvate. Also catalyzes the conversion of 4-carboxy-4-hydroxy-2-oxoadipic acid (CHA) to pyruvate and oxaloacetate.<ref>PMID:20843800</ref> <ref>PMID:24359411</ref>
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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/no/3noj_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=3noj 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 ==
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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.
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===The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3noj" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20843800}}, adds the Publication Abstract to the page
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*[[Aldolase 3D structures|Aldolase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 20843800 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20843800}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3NOJ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida_f1 Pseudomonas putida f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NOJ OCA].
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[[Category: Pseudomonas putida F1]]
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[[Category: Kimber MS]]
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==Reference==
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[[Category: Mazurkewich S]]
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<ref group="xtra">PMID:20843800</ref><references group="xtra"/>
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[[Category: Seah SYK]]
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[[Category: 4-hydroxy-4-methyl-2-oxoglutarate aldolase]]
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[[Category: Wang W]]
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[[Category: Pseudomonas putida f1]]
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[[Category: Kimber, M S.]]
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[[Category: Mazurkewich, S.]]
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[[Category: Seah, S Y.K.]]
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[[Category: Wang, W.]]
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[[Category: A-b-b-a sandwich]]
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[[Category: Class ii aldolase]]
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[[Category: Lyase]]
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[[Category: Metalloprotein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 6 05:39:34 2010''
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Current revision

The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida

PDB ID 3noj

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