6TTO

N-terminally truncated hyoscyamine 6-hydroxylase (tH6H) in complex with 2-oxoglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Regioselectivity of hyoscyamine 6 beta-hydroxylase-catalysed hydroxylation as revealed by high-resolution structural information and QM/MM calculations.

Kluza, A.Wojdyla, Z.Mrugala, B.Kurpiewska, K.Porebski, P.J.Niedzialkowska, E.Minor, W.Weiss, M.S.Borowski, T.

(2020) Dalton Trans 49: 4454-4469

  • DOI: https://doi.org/10.1039/d0dt00302f
  • Primary Citation of Related Structures:  
    6TTM, 6TTN, 6TTO

  • PubMed Abstract: 

    Hyoscyamine 6β-hydroxylase (H6H) is a bifunctional non-heme 2-oxoglutarate/Fe2+-dependent dioxygenase that catalyzes the two final steps in the biosynthesis of scopolamine. Based on high resolution crystal structures of H6H from Datura metel, detailed information on substrate binding was obtained that provided insights into the onset of the enzymatic process. In particular, the role of two prominent residues was revealed - Glu-116 that interacts with the tertiary amine located on the hyoscyamine tropane moiety and Tyr-326 that forms CH-π hydrogen bonds with the hyoscyamine phenyl ring. The structures were used as the basis for QM/MM calculations that provided an explanation for the regioselectivity of the hydroxylation reaction on the hyoscyamine tropane moiety (C6 vs. C7) and quantified contributions of active site residues to respective barrier heights.


  • Organizational Affiliation

    Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. ncborows@cyf-kr.edu.pl and Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hyoscyamine 6 beta-hydroxylase317Datura metelMutation(s): 0 
Gene Names: H6H
UniProt
Find proteins for Q6EZB3 (Datura metel)
Explore Q6EZB3 
Go to UniProtKB:  Q6EZB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6EZB3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG (Subject of Investigation/LOI)
Query on AKG

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

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O [auth A],
P [auth A]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
EDO
Query on EDO

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C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

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N [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FMT
Query on FMT

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M [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

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Q [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.896α = 90
b = 79.808β = 90
c = 104.437γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2014/14/E/NZ1/00053

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2020-04-15
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description