3axb

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[[Image:3axb.png|left|200px]]
 
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==Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix==
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The line below this paragraph, containing "STRUCTURE_3axb", creates the "Structure Box" on the page.
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<StructureSection load='3axb' size='340' side='right'caption='[[3axb]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
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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'>[[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>
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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]] 1.92&#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=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>
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{{STRUCTURE_3axb| PDB=3axb | 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=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>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix===
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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>
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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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The line below this paragraph, {{ABSTRACT_PUBMED_22511758}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3axb" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 22511758 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_22511758}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[3axb]] is a 1 chain structure with sequence from [http://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].
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==Reference==
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<ref group="xtra">PMID:022511758</ref><references group="xtra"/>
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[[Category: Aeropyrum pernix]]
[[Category: Aeropyrum pernix]]
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[[Category: Hara, Y.]]
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[[Category: Large Structures]]
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[[Category: Ohshima, T.]]
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[[Category: Hara Y]]
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[[Category: Sakuraba, H.]]
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[[Category: Ohshima T]]
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[[Category: Satomura, T.]]
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[[Category: Sakuraba H]]
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[[Category: Yoneda, K.]]
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[[Category: Satomura T]]
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[[Category: Dinucleotide-binding fold]]
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[[Category: Yoneda K]]
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[[Category: Oxidoreductase]]
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Current revision

Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix

PDB ID 3axb

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