Crystal structure of Fms1, a polyamine oxidase from Yeast

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

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This is version 1.2 of the entry. See complete history


Crystal Structures of Fms1 and its Complex with Spermine Reveal Substrate Specificity.

Huang, Q.Liu, Q.Hao, Q.

(2005) J Mol Biol 348: 951-959

  • DOI: https://doi.org/10.1016/j.jmb.2005.03.008
  • Primary Citation of Related Structures:  
    1RSG, 1XPQ, 1YY5

  • PubMed Abstract: 

    Fms1 is a rate-limiting enzyme for the biosynthesis of pantothenic acid in yeast. Fms1 has polyamine oxidase (PAO) activity, which converts spermine into spermidine and 3-aminopropanal. The 3-aminopropanal is further oxidized to produce beta-alanine, which is necessary for the biosynthesis of pantothenic acid. The crystal structures of Fms1 and its complex with the substrate spermine have been determined using the single-wavelength anomalous diffraction (SAD) phasing method. Fms1 consists of an FAD-binding domain, with Rossmann fold topology, and a substrate-binding domain. The active site is a tunnel located at the interface of the two domains. The substrate spermine binds to the active site mainly via hydrogen bonds and hydrophobic interactions. In the complex, C11 but not C9 of spermine is close enough to the catalytic site (N5 of FAD) to be oxidized. Therefore, the products are spermidine and 3-aminopropanal, rather than 3-(aminopropyl) 4-aminobutyraldehyde and 1,3-diaminoprone.

  • Organizational Affiliation

    MacCHESS at the Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853-8001, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FMS1 protein
A, B
513Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: FMS1
EC: (PDB Primary Data), (UniProt)
Find proteins for P50264 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50264 
Go to UniProtKB:  P50264
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50264
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C27 H33 N9 O15 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.711α = 90
b = 215.365β = 90
c = 118.157γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance