View source for 3axb


==Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix==
<StructureSection load='3axb' size='340' side='right'caption='[[3axb]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3axb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AXB FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.92&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</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=3axb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3axb OCA], [https://pdbe.org/3axb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3axb RCSB], [https://www.ebi.ac.uk/pdbsum/3axb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3axb ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
Two types of dye-linked l-proline dehydrogenase (PDH1, alpha4beta4-type hetero-octamer, and PDH2, alphabetagammadelta-type heterotetramer) have been identified so far in hyperthermophilic archaea. Here, we report the crystal structure of a third type of l-proline dehydrogenase, found in the aerobic hyperthermophilic archaeon Aeropyrum pernix, whose structure (homodimer) is much simpler than those of previously studied l-proline dehydrogenases. The structure was determined at a resolution of 1.92 A. The asymmetric unit contained one subunit, and a crystallographic 2-fold axis generated the functional dimer. The overall fold of the subunit showed similarity to that of the PDH1 beta-subunit, which is responsible for catalyzing l-proline dehydrogenation. However, the situation at the subunit-subunit interface of the A. pernix enzyme was totally different from that in PDH1. The presence of additional surface elements in the A. pernix enzyme contributes to a unique dimer association. Moreover, the C-terminal Leu(428), which is provided by a tail extending from the FAD-binding domain, shielded the active site, and an l-proline molecule was entrapped within the active site cavity. The K(m) value of a Leu(428) deletion mutant for l-proline was about 800 times larger than the K(m) value of the wild-type enzyme, although the k(cat) values did not differ much between the two enzymes. This suggests the C-terminal Leu(428) is not directly involved in catalysis, but it is essential for maintaining a high affinity for the substrate. This is the first description of an LPDH structure with l-proline bound, and it provides new insight into the substrate binding of LPDH.

Crystal Structure of Novel Dye-linked L-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix.,Sakuraba H, Satomura T, Kawakami R, Kim K, Hara Y, Yoneda K, Ohshima T J Biol Chem. 2012 Jun 8;287(24):20070-80. Epub 2012 Apr 16. PMID:22511758<ref>PMID:22511758</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
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</StructureSection>
[[Category: Aeropyrum pernix]]
[[Category: Large Structures]]
[[Category: Hara Y]]
[[Category: Ohshima T]]
[[Category: Sakuraba H]]
[[Category: Satomura T]]
[[Category: Yoneda K]]