4oe4: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4oe4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OE4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4oe4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OE4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.168&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=4oe4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oe4 OCA], [https://pdbe.org/4oe4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oe4 RCSB], [https://www.ebi.ac.uk/pdbsum/4oe4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oe4 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=4oe4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oe4 OCA], [https://pdbe.org/4oe4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oe4 RCSB], [https://www.ebi.ac.uk/pdbsum/4oe4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oe4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/PUT2_YEAST PUT2_YEAST]  
[https://www.uniprot.org/uniprot/PUT2_YEAST PUT2_YEAST]  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The proline catabolic enzyme Delta1-pyrroline-5-carboxylate dehydrogenase (ALDH4A1) catalyzes the NAD+-dependent oxidation of gamma-glutamate semialdehyde to l-glutamate. In Saccharomyces cerevisiae, ALDH4A1 is encoded by the PUT2 gene and known as Put2p. Here we report the steady-state kinetic parameters of the purified recombinant enzyme, two crystal structures of Put2p, and the determination of the oligomeric state and quaternary structure from small-angle X-ray scattering and sedimentation velocity. Using Delta1-pyrroline-5-carboxylate as the substrate, catalytic parameters kcat and Km were determined to be 1.5 s-1 and 104 muM, respectively, with a catalytic efficiency of 14000 M-1 s-1. Although Put2p exhibits the expected aldehyde dehydrogenase superfamily fold, a large portion of the active site is disordered in the crystal structure. Electron density for the 23-residue aldehyde substrate-binding loop is absent, implying substantial conformational flexibility in solution. We furthermore report a new crystal form of human ALDH4A1 (42% identical to Put2p) that also shows disorder in this loop. The crystal structures provide evidence of multiple active site conformations in the substrate-free form of the enzyme, which is consistent with a conformational selection mechanism of substrate binding. We also show that Put2p forms a trimer-of-dimers hexamer in solution. This result is unexpected because human ALDH4A1 is dimeric, whereas some bacterial ALDH4A1s are hexameric. Thus, global sequence identity and domain of life are poor predictors of the oligomeric states of ALDH4A1. Mutation of a single Trp residue that forms knob-in-hole interactions across the dimer-dimer interface abrogates hexamer formation, suggesting that this residue is the center of a protein-protein association hot spot.
Structural Studies of Yeast Delta-Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State.,Pemberton TA, Srivastava D, Sanyal N, Henzl MT, Becker DF, Tanner JJ Biochemistry. 2014 Feb 17. PMID:24502590<ref>PMID:24502590</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4oe4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Pyrroline-5-carboxylate dehydrogenase|Pyrroline-5-carboxylate dehydrogenase]]
*[[Pyrroline-5-carboxylate dehydrogenase|Pyrroline-5-carboxylate dehydrogenase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Latest revision as of 15:39, 1 March 2024

Crystal Structure of Yeast ALDH4A1 Complexed with NAD+Crystal Structure of Yeast ALDH4A1 Complexed with NAD+

Structural highlights

4oe4 is a 2 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.168Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PUT2_YEAST

See Also

4oe4, resolution 2.17Å

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