7K14 | pdb_00007k14

Ternary soak structure of alkanesulfonate monooxygenase MsuD from Pseudomonas fluorescens with FMN and methanesulfonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.214 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond cleavage, substrate scope, and an unexpected role for the tetramer.

Liew, J.J.M.El Saudi, I.M.Nguyen, S.V.Wicht, D.K.Dowling, D.P.

(2021) J Biological Chem 297: 100823-100823

  • DOI: https://doi.org/10.1016/j.jbc.2021.100823
  • Primary Citation Related Structures: 
    7JV3, 7JW9, 7JYB, 7K14, 7K64

  • PubMed Abstract: 

    Bacterial two-component flavin-dependent monooxygenases cleave the stable C-S bond of environmental and anthropogenic organosulfur compounds. The monooxygenase MsuD converts methanesulfonate (MS - ) to sulfite, completing the sulfur assimilation process during sulfate starvation, but the mechanism of this conversion remains unclear. To explore the mechanism of C-S bond cleavage, we report a series of crystal structures of MsuD from Pseudomonas fluorescens in different liganded states. This report provides the first crystal structures of an alkanesulfonate monooxygenase with a bound flavin and alkanesulfonate, elucidating the roles of the active site lid, the protein C terminus, and an active site loop in flavin and/or alkanesulfonate binding. These structures position MS - closest to the flavin N5 position, consistent with an N5-(hydro)peroxyflavin mechanism rather than a classical C4a-(hydro)peroxyflavin mechanism. A fully enclosed active site is observed in the ternary complex, mediated by interchain interaction of the C terminus at the tetramer interface. These structures identify an unexpected function of the protein C terminus in this protein family in stabilizing tetramer formation and the alkanesulfonate-binding site. Spurred by interest from the crystal structures, we conducted biochemical assays and molecular docking that redefine MsuD as a small- to medium-chain alkanesulfonate monooxygenase. Functional mutations verify the sulfonate-binding site and reveal the critical importance of the protein C terminus for monooxygenase function. These findings reveal a deeper understanding of MsuD's functionality at the molecular level and consequently how it operates within its role as part of the sulfur assimilation pathway.


  • Organizational Affiliation
    • Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA.

Macromolecule Content 

  • Total Structure Weight: 358.07 kDa 
  • Atom Count: 21,777 
  • Modeled Residue Count: 2,792 
  • Deposited Residue Count: 3,232 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alkanesulfonate monooxygenase
A, B, C, D, E
A, B, C, D, E, F, G, H
404Pseudomonas fluorescens Pf0-1Mutation(s): 0 
Gene Names: msuDssuDPfl01_3916
EC: 1.14.14.5
UniProt
Find proteins for Q3K9A1 (Pseudomonas fluorescens (strain Pf0-1))
Explore Q3K9A1 
Go to UniProtKB:  Q3K9A1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3K9A1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
T [auth G],
V [auth H]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
03S

Query on 03S



Download:Ideal Coordinates CCD File
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E]
methanesulfonic acid
C H4 O3 S
AFVFQIVMOAPDHO-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
S [auth F]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL

Query on CL



Download:Ideal Coordinates CCD File
U [auth G],
W [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.214 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94α = 90
b = 211.93β = 119.049
c = 94.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1807480

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2021-07-07
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description