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3w6u
From Proteopedia
(Difference between revisions)
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==Crystal structure of NADP bound L-serine 3-dehydrogenase from Hyperthermophilic Archaeon Pyrobaculum calidifontis== | ==Crystal structure of NADP bound L-serine 3-dehydrogenase from Hyperthermophilic Archaeon Pyrobaculum calidifontis== | ||
| - | <StructureSection load='3w6u' size='340' side='right' caption='[[3w6u]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='3w6u' size='340' side='right'caption='[[3w6u]], [[Resolution|resolution]] 2.00Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3w6u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrcj Pyrcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W6U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W6U FirstGlance]. <br> | <table><tr><td colspan='2'>[[3w6u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrcj Pyrcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W6U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W6U FirstGlance]. <br> | ||
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<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=3w6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w6u OCA], [http://pdbe.org/3w6u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w6u RCSB], [http://www.ebi.ac.uk/pdbsum/3w6u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w6u 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=3w6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w6u OCA], [http://pdbe.org/3w6u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w6u RCSB], [http://www.ebi.ac.uk/pdbsum/3w6u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w6u ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa L-SerDH. The overexpressed enzyme appears to be the most thermostable L-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 degrees C. The enzyme showed substantial reactivity towards D-serine, in addition to L-serine. Two different crystal structures of P. calidifontis L-SerDH were determined using the Se-MAD and MR method: the structure in complex with NADP(+)/sulfate ion at 1.18 A and the structure in complex with NADP(+)/L-tartrate (substrate analog) at 1.57 A. The fold of the catalytic domain showed similarity with that of Ps. aeruginosa L-SerDH. However, the active site structure significantly differed between the two enzymes. Based on the structure of the tartrate, L- and D-serine and 3-hydroxypropionate molecules were modeled into the active site and the substrate binding modes were estimated. A structural comparison suggests that the wide cavity at the substrate binding site is likely responsible for the high reactivity of the enzyme toward both L- and D-serine enantiomers. This is the first description of the structure of the novel type of L-SerDH with bound NADP(+) and substrate analog, and it provides new insight into the substrate binding mechanism of L-SerDH. The results obtained here may be very informative for the creation of L- or D-serine-specific SerDH by protein engineering. | ||
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| + | Crystal structure of the NADP(+) and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.,Yoneda K, Sakuraba H, Araki T, Ohshima T Extremophiles. 2018 Jan 20. pii: 10.1007/s00792-018-1004-0. doi:, 10.1007/s00792-018-1004-0. PMID:29353380<ref>PMID:29353380</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3w6u" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
| - | *[[6-phosphogluconate dehydrogenase|6-phosphogluconate dehydrogenase]] | + | *[[6-phosphogluconate dehydrogenase 3D structures|6-phosphogluconate dehydrogenase 3D structures]] |
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Pyrcj]] | [[Category: Pyrcj]] | ||
[[Category: Serine 3-dehydrogenase]] | [[Category: Serine 3-dehydrogenase]] | ||
Revision as of 07:53, 21 May 2019
Crystal structure of NADP bound L-serine 3-dehydrogenase from Hyperthermophilic Archaeon Pyrobaculum calidifontis
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