5FEU | pdb_00005feu

Noroxomaritidine/Norcraugsodine Reductase in complex with NADP+

• PDB DOI: https://doi.org/10.2210/pdb5FEU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Narcissus pseudonarcissus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-17 Released: 2016-06-08 
• Deposition Author(s): Holland, C., Jez, J.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Identification of a Noroxomaritidine Reductase with Amaryllidaceae Alkaloid Biosynthesis Related Activities.

Kilgore, M.B., Holland, C.K., Jez, J.M., Kutchan, T.M.

(2016) J Biological Chem 291: 16740-16752

• PubMed: 27252378 
• DOI: https://doi.org/10.1074/jbc.M116.717827
• Primary Citation Related Structures: 
  5FEU, 5FF9, 5FFF


• PubMed Abstract: 
  

  Amaryllidaceae alkaloids are a large group of plant natural products with over 300 documented structures and diverse biological activities. Several groups of Amaryllidaceae alkaloids including the hemanthamine- and crinine-type alkaloids show promise as anticancer agents. Two reduction reactions are required for the production of these compounds: the reduction of norcraugsodine to norbelladine and the reduction of noroxomaritidine to normaritidine, with the enantiomer of noroxomaritidine dictating whether the derivatives will be the crinine-type or hemanthamine-type. It is also possible for the carbon-carbon double bond of noroxomaritidine to be reduced, forming the precursor for maritinamine or elwesine depending on the enantiomer reduced to an oxomaritinamine product. In this study, a short chain alcohol dehydrogenase/reductase that co-expresses with the previously discovered norbelladine 4'-O-methyltransferase from Narcissus sp. and Galanthus spp. was cloned and expressed in Escherichia coli Biochemical analyses and x-ray crystallography indicates that this protein functions as a noroxomaritidine reductase that forms oxomaritinamine from noroxomaritidine through a carbon-carbon double bond reduction. The enzyme also reduces norcraugsodine to norbelladine with a 400-fold lower specific activity. These studies identify a missing step in the biosynthesis of this pharmacologically important class of plant natural products.

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Organizational Affiliation: 
• From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132 and the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130.
the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130.
From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132 and [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 31.93 kDa 
• Atom Count: 2,063 
• Modeled Residue Count: 246 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Noroxomaritidine/Norcraugsodine Reductase	A	291	Narcissus pseudonarcissus	Mutation(s): 0  EC: 1.1.1
UniProt
Find proteins for A0A1A9TAK5 (Narcissus pseudonarcissus) Explore A0A1A9TAK5  Go to UniProtKB:  A0A1A9TAK5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.377	α = 90
b = 60.377	β = 90
c = 136.142	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
SCALEPACK	data scaling
PHASER	phasing
HKL-3000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Holland, C., Jez, J.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1RC2GM092561

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references
• Version 1.2: 2016-08-17
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description