4ECH

Yeast Polyamine Oxidase FMS1, H67Q Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Literature

Mechanistic and structural analyses of the role of his67 in the yeast polyamine oxidase fms1.

Adachi, M.S.Taylor, A.B.Hart, P.J.Fitzpatrick, P.F.

(2012) Biochemistry 51: 4888-4897

  • DOI: https://doi.org/10.1021/bi300517s
  • Primary Citation of Related Structures:  
    4ECH

  • PubMed Abstract: 

    The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N(1)-acetylspermine to spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. Within the active site of Fms1, His67 is positioned to form hydrogen bonds with the polyamine substrate. This residue is also conserved in other polyamine oxidases. The catalytic properties of H67Q, H67N, and H67A Fms1 have been characterized to evaluate the role of this residue in catalysis. With both spermine and N(1)-acetylspermine as the amine substrate, the value of the first-order rate constant for flavin reduction decreases 2-3 orders of magnitude, with the H67Q mutation having the smallest effect and H67N the largest. The k(cat)/K(O2) value changes very little upon mutation with N(1)-acetylspermine as the amine substrate and decreases only an order of magnitude with spermine. The k(cat)/K(M)-pH profiles with N(1)-acetylspermine are bell-shaped for all the mutants; the similarity to the profile of the wild-type enzyme rules out His67 as being responsible for either of the pK(a) values. The pH profiles for the rate constant for flavin reduction for all the mutant enzymes similarly show the same pK(a) as wild-type Fms1, about ∼7.4; this pK(a) is assigned to the substrate N4. The k(cat)/K(O2)-pH profiles for wild-type Fms1 and the H67A enzyme both show a pK(a) of about ∼6.9; this suggests His67 is not responsible for this pH behavior. With the H67Q, H67N, and H67A enzymes the k(cat) value decreases when a single residue is protonated, as is the case with the wild-type enzyme. The structure of H67Q Fms1 has been determined at a resolution of 2.4 Å. The structure shows that the mutation disrupts a hydrogen bond network in the active site, suggesting that His67 is important both for direct interactions with the substrate and to maintain the overall active site structure.


  • Organizational Affiliation

    Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyamine oxidase FMS1
A, B
516Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: FMS1YM9711.09YMR020W
EC: 1.5.3.17
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.16α = 90
b = 102β = 93.12
c = 75.83γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-20
    Changes: Data collection, Refinement description