3q3c: Difference between revisions
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<StructureSection load='3q3c' size='340' side='right'caption='[[3q3c]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='3q3c' size='340' side='right'caption='[[3q3c]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3q3c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3q3c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q3C FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.299Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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=3q3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q3c OCA], [https://pdbe.org/3q3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q3c RCSB], [https://www.ebi.ac.uk/pdbsum/3q3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q3c ProSAT]</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=3q3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q3c OCA], [https://pdbe.org/3q3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q3c RCSB], [https://www.ebi.ac.uk/pdbsum/3q3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q3c ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/SERDH_PSEAE SERDH_PSEAE] NAD-dependent L-serine dehydrogenase that catalyzes the oxidation of L-serine and methyl-L-serine and is possibly involved in serine catabolism. Has low activity toward beta-hydroxyisobutyrate.<ref>PMID:22128181</ref> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Pseudomonas aeruginosa]] | ||
[[Category: Edwards | [[Category: Edwards AM]] | ||
[[Category: Evdokimova | [[Category: Evdokimova E]] | ||
[[Category: Joachimiak | [[Category: Joachimiak A]] | ||
[[Category: Kudritska | [[Category: Kudritska M]] | ||
[[Category: Savchenko A]] | |||
[[Category: Savchenko | [[Category: Singer AU]] | ||
[[Category: Singer | [[Category: Tan K]] | ||
[[Category: Tan | [[Category: Yakunin AF]] | ||
[[Category: Yakunin | |||
Latest revision as of 12:35, 30 October 2024
Crystal structure of a serine dehydrogenase from Pseudomonas aeruginosa pao1 in complex with NADCrystal structure of a serine dehydrogenase from Pseudomonas aeruginosa pao1 in complex with NAD
Structural highlights
FunctionSERDH_PSEAE NAD-dependent L-serine dehydrogenase that catalyzes the oxidation of L-serine and methyl-L-serine and is possibly involved in serine catabolism. Has low activity toward beta-hydroxyisobutyrate.[1] Publication Abstract from PubMedThe beta-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various beta-hydroxy acid substrates to corresponding semialdehydes. Several known enzymes include beta-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of beta-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted beta-hydroxyisobutyrate dehydrogenase PA0743 from Pseudomonas aeruginosa catalyzes an NAD(+)-dependent oxidation of l-serine and methyl-l-serine but exhibits low activity against beta-hydroxyisobutyrate. Two crystal structures of PA0743 were solved at 2.2-2.3-A resolution and revealed an N-terminal Rossmann fold domain connected by a long alpha-helix to the C-terminal all-alpha domain. The PA0743 apostructure showed the presence of additional density modeled as HEPES bound in the interdomain cleft close to the predicted catalytic Lys-171, revealing the molecular details of the PA0743 substrate-binding site. The structure of the PA0743-NAD(+) complex demonstrated that the opposite side of the enzyme active site accommodates the cofactor, which is also bound near Lys-171. Site-directed mutagenesis of PA0743 emphasized the critical role of four amino acid residues in catalysis including the primary catalytic residue Lys-171. Our results provide further insight into the molecular mechanisms of substrate selectivity and activity of beta-hydroxyacid dehydrogenases. Biochemical and Structural Studies of Uncharacterized Protein PA0743 from Pseudomonas aeruginosa Revealed NAD+-dependent L-Serine Dehydrogenase.,Tchigvintsev A, Singer A, Brown G, Flick R, Evdokimova E, Tan K, Gonzalez CF, Savchenko A, Yakunin AF J Biol Chem. 2012 Jan 13;287(3):1874-83. Epub 2011 Nov 28. PMID:22128181[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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