4qdf: Difference between revisions
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New page: '''Unreleased structure''' The entry 4qdf is ON HOLD Authors: Penfield, J., Worrall, L.J., Strynadka, N.C., Eltis, L.D. Description: Crystal structure of apo KshA5 and KshA1 in complex... |
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==Crystal structure of apo KshA5 and KshA1 in complex with 1,4-30Q-CoA from R. rhodochrous== | |||
<StructureSection load='4qdf' size='340' side='right'caption='[[4qdf]], [[Resolution|resolution]] 2.43Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4qdf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_rhodochrous Rhodococcus rhodochrous]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QDF 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]] 2.43Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=30Q:S-[2-(PROPANOYLAMINO)ETHYL]+(2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-DIMETHYL-3-OXO-6,7,8,9,10,11,12,13,14,15,16,17-DODECAHYDRO-3H-CYCLOPENTA[A]PHENANTHREN-17-YL]PROPANETHIOATE+(NON-PREFERRED+NAME)'>30Q</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdf OCA], [https://pdbe.org/4qdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qdf RCSB], [https://www.ebi.ac.uk/pdbsum/4qdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qdf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/KSHA5_RHORH KSHA5_RHORH] Probably involved in the degradation of cholesterol (PubMed:21642460). In vitro, catalyzes the introduction of a 9alpha-hydroxyl moiety into the ring B of 3-ketosteroid substrates such as 1,4-androstadiene-3,17-dione (ADD), 4-androstene-3,17-dione (AD), 4-androstene-17beta-ol-3-one (testosterone), 4-pregnene-3,20-dione (progesterone), 19-nor-4-androstene-3,17-dione, 1-(5alpha)-androstene-3,17-dione, 5alpha-androstane-3,17-dione, 5beta-androstane-3,17-dione, 5alpha-androstane-17beta-ol-3-one (stanolon), 11beta-hydrocortisone, 3-oxo-23,24-bisnorcholesta-4-en-22-oate (4-BNC), 23,24-bisnorcholesta-4-ene-22-oate, 3-oxo-23,24-bisnorcholesta-1,4-dien-22-oate (1,4-BNC) and 3-oxo-23,24-bisnorcholesta-1,4-dien-22-oyl-coenzyme A thioester (1,4-BNC-CoA) (PubMed:21642460, PubMed:25049233). KshA5 has the broadest substrate range without a clear substrate preference and is active with Delta-4, Delta-1,4, 5alpha-H and 5beta-H steroids, as well as with steroids having bulky aliphatic side chains and an isopropionyl side chain at C17.<ref>PMID:21642460</ref> <ref>PMID:25049233</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
KshA is the oxygenase component of 3-ketosteroid 9alpha-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >10(5) s(-1) m(-1) for 4-estrendione, 5alpha-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (Ki S approximately 100 mum). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb.ADD, KshA1.1,4-BNC-CoA, KshA5.ADD, and KshA5.1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue "mouth loop," which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and alpha-helices harboring its ligands were displaced up to 4.4 A in the KshA5.substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450. | |||
Substrate specificities and conformational flexibility of 3-ketosteroid 9alpha-hydroxylases.,Penfield JS, Worrall LJ, Strynadka NC, Eltis LD J Biol Chem. 2014 Sep 12;289(37):25523-36. doi: 10.1074/jbc.M114.575886. Epub, 2014 Jul 21. PMID:25049233<ref>PMID:25049233</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4qdf" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Rhodococcus rhodochrous]] | |||
[[Category: Eltis LD]] | |||
[[Category: Penfield J]] | |||
[[Category: Strynadka NC]] | |||
[[Category: Worrall LJ]] | |||
