3tkt: Difference between revisions
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==Crystal structure of CYP108D1 from Novosphingobium aromaticivorans DSM12444== | ==Crystal structure of CYP108D1 from Novosphingobium aromaticivorans DSM12444== | ||
<StructureSection load='3tkt' size='340' side='right' caption='[[3tkt]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='3tkt' size='340' side='right' caption='[[3tkt]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3tkt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3tkt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Novad Novad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TKT FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Saro_3162 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Saro_3162 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=279238 NOVAD])</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=3tkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tkt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tkt RCSB], [http://www.ebi.ac.uk/pdbsum/3tkt PDBsum]</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=3tkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tkt OCA], [http://pdbe.org/3tkt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tkt RCSB], [http://www.ebi.ac.uk/pdbsum/3tkt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tkt ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3tkt" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Novad]] | ||
[[Category: Bartlam, M]] | [[Category: Bartlam, M]] | ||
[[Category: Bell, S G]] | [[Category: Bell, S G]] | ||
Revision as of 22:09, 10 December 2016
Crystal structure of CYP108D1 from Novosphingobium aromaticivorans DSM12444Crystal structure of CYP108D1 from Novosphingobium aromaticivorans DSM12444
Structural highlights
Publication Abstract from PubMedCYP108D1 from Novosphingobium aromaticivorans DSM12444 binds a range of aromatic hydrocarbons such as phenanthrene, biphenyl and phenylcyclohexane. Its structure, which is reported here at 2.2 A resolution, is closely related to that of CYP108A1 (P450terp), an alpha-terpineol-oxidizing enzyme. The compositions and structures of the active sites of these two enzymes are very similar; the most significant changes are the replacement of Glu77 and Thr103 in CYP108A1 by Thr79 and Val105 in CYP108D1. Other residue differences lead to a larger and more hydrophobic access channel in CYP108D1. These structural features are likely to account for the weaker alpha-terpineol binding by CYP108D1 and, when combined with the presence of three hydrophobic phenylalanine residues in the active site, promote the binding of aromatic hydrocarbons. The haem-proximal surface of CYP108D1 shows a different charge distribution and topology to those of CYP101D1, CYP101A1 and CYP108A1, including a pronounced kink in the proximal loop of CYP108D1, which may result in poor complementarity with the [2Fe-2S] ferredoxins Arx, putidaredoxin and terpredoxin that are the respective redox partners of these three P450 enzymes. The unexpectedly low reduction potential of phenylcyclohexane-bound CYP108D1 (-401 mV) may also contribute to the low activity observed with these ferredoxins. CYP108D1 appears to function as an aromatic hydrocarbon hydroxylase that requires a different electron-transfer cofactor protein. Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme.,Bell SG, Yang W, Yorke JA, Zhou W, Wang H, Harmer J, Copley R, Zhang A, Zhou R, Bartlam M, Rao Z, Wong LL Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):277-91. Epub 2012 Feb 14. PMID:22349230[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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