6TTM | pdb_00006ttm

Hyoscyamine 6-hydroxylase in complex with N-oxalylglycine and hyoscyamine

• PDB DOI: https://doi.org/10.2210/pdb6TTM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Datura metel
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-29 Released: 2020-03-18 
• Deposition Author(s): Kluza, A., Kurpiewska, K., Mrugala, B., Porebski, P.J., Niedzialkowska, E., Minor, W., Borowski, T.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.200 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

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

• PubMed: 32182320 
• DOI: https://doi.org/10.1039/d0dt00302f
• Primary Citation 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.

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Organizational Affiliation: 
• Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. [e-mail].
Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. [e-mail] and Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL-30387 Krakow, Poland.
Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. [e-mail] and Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA.
Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA.
Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, D-12489, Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.68 kDa 
• Atom Count: 2,679 
• Modeled Residue Count: 299 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyoscyamine 6 beta-hydroxylase	A	350	Datura metel	Mutation(s): 0  Gene Names: H6H
UniProt
Find proteins for Q6EZB3 (Datura metel) Explore Q6EZB3  Go to UniProtKB:  Q6EZB3

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HYO (Subject of Investigation/LOI)	C [auth A]	[(1S,5R)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2S)-3-hydroxy-2-phenylpropanoate C17 H23 N O3 RKUNBYITZUJHSG-FXUDXRNXSA-N
OGA (Subject of Investigation/LOI)	E [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SR	H [auth A]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N
EDO	F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
UNX	I [auth A], J [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.200 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.536	α = 90
b = 70.78	β = 90
c = 78.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MoRDa	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Kluza, A., Kurpiewska, K., Mrugala, B., Porebski, P.J., Niedzialkowska, E., Minor, W., Borowski, T.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2014/14/E/NZ1/00053

Revision History  

• 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