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4qdd

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Revision as of 11:24, 15 February 2023

Crystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) from R. rhodochrous in complex with 1,4-30Q-CoA

Structural highlights

4qdd is a 1 chain structure with sequence from Rhodococcus rhodochrous. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2]

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Petrusma M, Hessels G, Dijkhuizen L, van der Geize R. Multiplicity of 3-Ketosteroid-9α-Hydroxylase enzymes in Rhodococcus rhodochrous DSM43269 for specific degradation of different classes of steroids. J Bacteriol. 2011 Aug;193(15):3931-40. PMID:21642460 doi:10.1128/JB.00274-11
↑ Penfield JS, Worrall LJ, Strynadka NC, Eltis LD. Substrate specificities and conformational flexibility of 3-ketosteroid 9alpha-hydroxylases. J Biol Chem. 2014 Sep 12;289(37):25523-36. doi: 10.1074/jbc.M114.575886. Epub, 2014 Jul 21. PMID:25049233 doi:http://dx.doi.org/10.1074/jbc.M114.575886
↑ Penfield JS, Worrall LJ, Strynadka NC, Eltis LD. Substrate specificities and conformational flexibility of 3-ketosteroid 9alpha-hydroxylases. J Biol Chem. 2014 Sep 12;289(37):25523-36. doi: 10.1074/jbc.M114.575886. Epub, 2014 Jul 21. PMID:25049233 doi:http://dx.doi.org/10.1074/jbc.M114.575886

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4qdd"

@@ Line 1: / Line 1: @@
 ==Crystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) from R. rhodochrous in complex with 1,4-30Q-CoA==
-<StructureSection load='4qdd' size='340' side='right' caption='[[4qdd]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='4qdd' size='340' side='right'caption='[[4qdd]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4qdd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_mycoides_roseum"_grotenfelt_1889 "bacterium mycoides roseum" grotenfelt 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QDD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4qdd]] is a 1 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=4QDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QDD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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></td></tr>
+</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></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qdc|4qdc]], [[4qdf|4qdf]], [[4qck|4qck]]</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=4qdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdd OCA], [https://pdbe.org/4qdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qdd RCSB], [https://www.ebi.ac.uk/pdbsum/4qdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qdd ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kshA5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1829 "Bacterium mycoides roseum" Grotenfelt 1889])</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=4qdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdd OCA], [http://pdbe.org/4qdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qdd RCSB], [http://www.ebi.ac.uk/pdbsum/4qdd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qdd 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 ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bacterium mycoides roseum grotenfelt 1889]]
+[[Category: Large Structures]]
-[[Category: Eltis, L D]]
+[[Category: Rhodococcus rhodochrous]]
-[[Category: Penfield, J]]
+[[Category: Eltis LD]]
-[[Category: Strynadka, N C]]
+[[Category: Penfield J]]
-[[Category: Worrall, L J]]
+[[Category: Strynadka NC]]
-[[Category: Mixed function oxygenase]]
+[[Category: Worrall LJ]]
-[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]

4qdd

From Proteopedia

Revision as of 11:24, 15 February 2023

Crystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) from R. rhodochrous in complex with 1,4-30Q-CoA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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