6UUG | pdb_00006uug

Structure of methanesulfinate monooxygenase MsuC from Pseudomonas fluorescens at 1.69 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6UUG/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Pseudomonas fluorescens Pf0-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-30 Released: 2019-12-04 
• Deposition Author(s): Soule, J., Gnann, A.D., Gonzalez, R., Parker, M.J., McKenna, K.C., Nguyen, S.V., Phan, N.T., Wicht, D.K., Dowling, D.P.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Structure and function of the two-component flavin-dependent methanesulfinate monooxygenase within bacterial sulfur assimilation.

Soule, J., Gnann, A.D., Gonzalez, R., Parker, M.J., McKenna, K.C., Nguyen, S.V., Phan, N.T., Wicht, D.K., Dowling, D.P.

(2020) Biochem Biophys Res Commun 522: 107-112

• PubMed: 31753487 
• DOI: https://doi.org/10.1016/j.bbrc.2019.11.008
• Primary Citation Related Structures: 
  6UUG


• PubMed Abstract: 
  

  Methyl sulfur compounds are a rich source of environmental sulfur for microorganisms, but their use requires redox systems. The bacterial sfn and msu operons contain two-component flavin-dependent monooxygenases for dimethylsulfone (DMSO ₂ ) assimilation: SfnG converts DMSO ₂ to methanesulfinate (MSI ^- ), and MsuD converts methanesulfonate (MS ^- ) to sulfite. However, the enzymatic oxidation of MSI ^- to MS ^- has not been demonstrated, and the function of the last enzyme of the msu operon (MsuC) is unresolved. We employed crystallographic and biochemical studies to identify the function of MsuC from Pseudomonas fluorescens. The crystal structure of MsuC adopts the acyl-CoA dehydrogenase fold with putative binding sites for flavin and MSI ^- , and functional assays of MsuC in the presence of its oxidoreductase MsuE, FMN, and NADH confirm the enzymatic generation of MS ^- . These studies reveal that MsuC converts MSI ^- to MS ^- in sulfite biosynthesis from DMSO ₂ .

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Organizational Affiliation: 
• Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA.
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Department of Chemistry and Biochemistry, Suffolk University, Boston, MA, 02108, USA.
Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA; Department of Chemistry and Biochemistry, Suffolk University, Boston, MA, 02108, USA.
Department of Chemistry and Biochemistry, Suffolk University, Boston, MA, 02108, USA. Electronic address: [e-mail].
Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA. Electronic address: [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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 92.52 kDa 
• Atom Count: 6,483 
• Modeled Residue Count: 774 
• Deposited Residue Count: 830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dehydrogenase	A, B	415	Pseudomonas fluorescens Pf0-1	Mutation(s): 0  Gene Names: Pfl01_3917
UniProt
Find proteins for Q3K9A0 (Pseudomonas fluorescens (strain Pf0-1)) Explore Q3K9A0  Go to UniProtKB:  Q3K9A0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.187	α = 90
b = 161.582	β = 90
c = 62.045	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Soule, J., Gnann, A.D., Gonzalez, R., Parker, M.J., McKenna, K.C., Nguyen, S.V., Phan, N.T., Wicht, D.K., Dowling, D.P.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1807480

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2020-01-22
  Changes: Database references
• Version 1.3: 2020-05-06
  Changes: Structure summary
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description