1FML

CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN A COMPLEX WITH RETINOL AND PAP

• PDB DOI: https://doi.org/10.2210/pdb1FML/pdb

• Classification: TRANSFERASE
• Organism(s): Spodoptera frugiperda
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-08-17 Released: 2001-05-02 
• Deposition Author(s): Pakhomova, S., Kobayashi, M., Buck, J., Newcomer, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.273 
• R-Value Work: 0.222 

Literature

A helical lid converts a sulfotransferase to a dehydratase.

Pakhomova, S., Kobayashi, M., Buck, J., Newcomer, M.E.

(2001) Nat Struct Biol 8: 447-451

• PubMed: 11323722 
• DOI: https://doi.org/10.1038/87617
• Primary Citation of Related Structures:  
  1FMJ, 1FML


• PubMed Abstract: 
  

  We report here the crystal structure of retinol dehydratase, an enzyme that catalyzes the synthesis of anhydroretinol. The enzyme is a member of the sulfotransferase superfamily and its crystal structure reveals the insertion of a helical lid into a canonical sulfotransferase fold. Site-directed mutations demonstrate that this inserted lid is necessary for anhydroretinol production but not for sulfonation; thus, insertion of a helical lid can convert a sulfotransferase into a dehydratase.

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Organizational Affiliation: 

Biochemistry Department, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 84.62 kDa 
• Atom Count: 5,859 
• Modelled Residue Count: 682 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RETINOL DEHYDRATASE	A, B	351	Spodoptera frugiperda	Mutation(s): 0
UniProt
Find proteins for Q26490 (Spodoptera frugiperda) Explore Q26490  Go to UniProtKB:  Q26490

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P	D [auth A], G [auth B]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N
RTL	E [auth A], H [auth B]	RETINOL C20 H30 O FPIPGXGPPPQFEQ-OVSJKPMPSA-N
CA	C [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.273 
• R-Value Work: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.053	α = 90
b = 66.612	β = 111.29
c = 84.904	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-02 
Deposition Author(s): Pakhomova, S., Kobayashi, M., Buck, J., Newcomer, M.E.

Revision History  

• Version 1.0: 2001-05-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations