3BHF | pdb_00003bhf

Crystal structure of R49K mutant of Monomeric Sarcosine Oxidase crystallized in PEG as precipitant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.251 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Arginine 49 is a bifunctional residue important in catalysis and biosynthesis of monomeric sarcosine oxidase: a context-sensitive model for the electrostatic impact of arginine to lysine mutations.

Hassan-Abdallah, A.Zhao, G.Chen, Z.W.Mathews, F.S.Schuman Jorns, M.

(2008) Biochemistry 47: 2913-2922

  • DOI: https://doi.org/10.1021/bi702351v
  • Primary Citation Related Structures: 
    3BHF, 3BHK

  • PubMed Abstract: 

    Monomeric sarcosine oxidase (MSOX) contains covalently bound FAD and catalyzes the oxidative demethylation of sarcosine ( N-methylglycine). The side chain of Arg49 is in van der Waals contact with the si face of the flavin ring; sarcosine binds just above the re face. Covalent flavin attachment requires a basic residue (Arg or Lys) at position 49. Although flavinylation is scarcely affected, mutation of Arg49 to Lys causes a 40-fold decrease in k cat and a 150-fold decrease in k cat/ K m sarcosine. The overall structure of the Arg49Lys mutant is very similar to wild-type MSOX; the side chain of Lys49 in the mutant is nearly congruent to that of Arg49 in the wild-type enzyme. The Arg49Lys mutant exhibits several features consistent with a less electropositive active site: (1) Charge transfer bands observed for mutant enzyme complexes with competitive inhibitors absorb at higher energy than the corresponding wild-type complexes. (2) The p K a for ionization at N(3)H of FAD is more than two pH units higher in the mutant than in wild-type MSOX. (3) The reduction potential of the oxidized/radical couple in the mutant is 100 mV lower than in the wild-type enzyme. The lower reduction potential is likely to be a major cause of the reduced catalytic activity of the mutant. Electrostatic interactions with Arg49 play an important role in catalysis and covalent flavinylation. A context-sensitive model for the electrostatic impact of an arginine to lysine mutation can account for the dramatically different consequences of the Arg49Lys mutation on MSOX catalysis and holoenzyme biosysnthesis.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.

Macromolecule Content 

  • Total Structure Weight: 88.05 kDa 
  • Atom Count: 6,434 
  • Modeled Residue Count: 762 
  • Deposited Residue Count: 780 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Monomeric sarcosine oxidase
A, B
390Bacillus sp. (in: firmicutes)Mutation(s): 1 
Gene Names: soxAsox
EC: 1.5.3.1
UniProt
Find proteins for P40859 (Bacillus sp. (strain B-0618))
Explore P40859 
Go to UniProtKB:  P40859
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40859
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.348α = 90
b = 70.456β = 96.77
c = 79.595γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary