8CVG

Structure of L289F Hyoscyamine 6-beta Hydroxylase in complex with iron, 2-oxoglutarate, and 6-OH-hyoscyamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.201 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.190 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted OVRClick on this verticalbar to view detailsBest fitted AKGClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Optimized Substrate Positioning Enables Switches in the C-H Cleavage Site and Reaction Outcome in the Hydroxylation-Epoxidation Sequence Catalyzed by Hyoscyamine 6 beta-Hydroxylase.

Wenger, E.S.Martinie, R.J.Ushimaru, R.Pollock, C.J.Sil, D.Li, A.Hoang, N.Palowitch, G.M.Graham, B.P.Schaperdoth, I.Burke, E.J.Maggiolo, A.O.Chang, W.C.Allen, B.D.Krebs, C.Silakov, A.Boal, A.K.Bollinger Jr., J.M.

(2024) J Am Chem Soc 146: 24271-24287

  • DOI: https://doi.org/10.1021/jacs.4c04406
  • Primary Citation of Related Structures:  
    8CV8, 8CV9, 8CVA, 8CVB, 8CVC, 8CVD, 8CVE, 8CVF, 8CVG, 8CVH

  • PubMed Abstract: 

    Hyoscyamine 6β-hydroxylase (H6H) is an iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase that produces the prolifically administered antinausea drug, scopolamine. After its namesake hydroxylation reaction, H6H then couples the newly installed C6 oxygen to C7 to produce the drug's epoxide functionality. Oxoiron(IV) (ferryl) intermediates initiate both reactions by cleaving C-H bonds, but it remains unclear how the enzyme switches the target site and promotes (C6)O-C7 coupling in preference to C7 hydroxylation in the second step. In one possible epoxidation mechanism, the C6 oxygen would─analogously to mechanisms proposed for the Fe/2OG halogenases and, in our more recent study, N -acetylnorloline synthase (LolO)─coordinate as alkoxide to the C7-H-cleaving ferryl intermediate to enable alkoxyl coupling to the ensuing C7 radical. Here, we provide structural and kinetic evidence that H6H does not employ substrate coordination or repositioning for the epoxidation step but instead exploits the distinct spatial dependencies of competitive C-H cleavage (C6 vs C7) and C-O-coupling (oxygen rebound vs cyclization) steps to promote the two-step sequence. Structural comparisons of ferryl-mimicking vanadyl complexes of wild-type H6H and a variant that preferentially 7-hydroxylates instead of epoxidizing 6β-hydroxyhyoscyamine suggest that a modest (∼10°) shift in the Fe-O-H(C7) approach angle is sufficient to change the outcome. The 7-hydroxylation:epoxidation partition ratios of both proteins increase more than 5-fold in 2 H 2 O, reflecting an epoxidation-specific requirement for cleavage of the alcohol O-H bond, which, unlike in the LolO oxacyclization, is not accomplished by iron coordination in advance of C-H cleavage.


  • Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hyoscyamine 6-beta-hydroxylase385Atropa belladonnaMutation(s): 1 
Gene Names: AbH6Hh6h
EC: 1.14.11.11
UniProt
Find proteins for Q9XJ43 (Atropa belladonna)
Explore Q9XJ43 
Go to UniProtKB:  Q9XJ43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XJ43
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OVR (Subject of Investigation/LOI)
Query on OVR

Download Ideal Coordinates CCD File 
J [auth A](1R,3S,5R,6S)-6-hydroxy-8-methyl-8-azabicyclo[3.2.1]octan-3-yl (2S)-3-hydroxy-2-phenylpropanoate
C17 H23 N O4
WTQYWNWRJNXDEG-RBZJEDDUSA-N
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
F [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
SR
Query on SR

Download Ideal Coordinates CCD File 
U [auth A],
V [auth A]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
G [auth A]
L [auth A]
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
FMT
Query on FMT

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E [auth A]
H [auth A]
I [auth A]
K [auth A]
M [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.719α = 90
b = 79.228β = 111.027
c = 55.822γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted OVRClick on this verticalbar to view detailsBest fitted AKGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM113106

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references, Structure summary