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| ==The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida== | | ==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=''> | + | <StructureSection load='3noj' size='340' side='right'caption='[[3noj]], [[Resolution|resolution]] 1.82Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[3noj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Psep1 Psep1]. 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> | + | <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> |
- | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.82Å</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=351746 PSEP1])</td></tr> | + | <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> |
- | <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'>[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> |
- | <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://pdbe.org/3noj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3noj RCSB], [http://www.ebi.ac.uk/pdbsum/3noj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3noj ProSAT]</span></td></tr> | + | |
| </table> | | </table> |
| == Function == | | == Function == |
- | [[http://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> | + | [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> |
| == Evolutionary Conservation == | | == Evolutionary Conservation == |
| [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| ==See Also== | | ==See Also== |
- | *[[Aldolase|Aldolase]] | + | *[[Aldolase 3D structures|Aldolase 3D structures]] |
| == References == | | == References == |
| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
- | [[Category: 4-hydroxy-4-methyl-2-oxoglutarate aldolase]] | + | [[Category: Large Structures]] |
- | [[Category: Psep1]] | + | [[Category: Pseudomonas putida F1]] |
- | [[Category: Kimber, M S]] | + | [[Category: Kimber MS]] |
- | [[Category: Mazurkewich, S]] | + | [[Category: Mazurkewich S]] |
- | [[Category: Seah, S Y.K]] | + | [[Category: Seah SYK]] |
- | [[Category: Wang, W]] | + | [[Category: Wang W]] |
- | [[Category: A-b-b-a sandwich]]
| + | |
- | [[Category: Class ii aldolase]]
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- | [[Category: Lyase]]
| + | |
- | [[Category: Metalloprotein]]
| + | |
| Structural highlights
Function
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.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wang W, Mazurkewich S, Kimber MS, Seah SY. 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. J Biol Chem. 2010 Sep 15. PMID:20843800 doi:10.1074/jbc.M110.159509
- ↑ Mazurkewich S, Wang W, Seah SY. Biochemical and structural analysis of RraA proteins to decipher their relationships with 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolases. Biochemistry. 2014 Jan 28;53(3):542-53. doi: 10.1021/bi401486g. Epub 2014 Jan 10. PMID:24359411 doi:http://dx.doi.org/10.1021/bi401486g
- ↑ Wang W, Mazurkewich S, Kimber MS, Seah SY. 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. J Biol Chem. 2010 Sep 15. PMID:20843800 doi:10.1074/jbc.M110.159509
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