4F07

Structure of the Styrene Monooxygenase Flavin Reductase (SMOB) from Pseudomonas putida S12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure and Mechanism of Styrene Monooxygenase Reductase: New Insight into the FAD-Transfer Reaction.

Morrison, E.Kantz, A.Gassner, G.T.Sazinsky, M.H.

(2013) Biochemistry 52: 6063-6075

  • DOI: https://doi.org/10.1021/bi400763h
  • Primary Citation of Related Structures:  
    4F07

  • PubMed Abstract: 

    The two-component flavoprotein styrene monooxygenase (SMO) from Pseudomonas putida S12 catalyzes the NADH- and FAD-dependent epoxidation of styrene to styrene oxide. In this study, we investigate the mechanism of flavin reduction and transfer from the reductase (SMOB) to the epoxidase (NSMOA) component and report our findings in light of the 2.2 Å crystal structure of SMOB. Upon rapidly mixing with NADH, SMOB forms an NADH → FADox charge-transfer intermediate and catalyzes a hydride-transfer reaction from NADH to FAD, with a rate constant of 49.1 ± 1.4 s(-1), in a step that is coupled to the rapid dissociation of NAD(+). Electrochemical and equilibrium-binding studies indicate that NSMOA binds FADhq ∼13-times more tightly than SMOB, which supports a vectoral transfer of FADhq from the reductase to the epoxidase. After binding to NSMOA, FADhq rapidly reacts with molecular oxygen to form a stable C(4a)-hydroperoxide intermediate. The half-life of apoSMOB generated in the FAD-transfer reaction is increased ∼21-fold, supporting a protein-protein interaction between apoSMOB and the peroxide intermediate of NSMOA. The mechanisms of FAD dissociation and transport from SMOB to NSMOA were probed by monitoring the competitive reduction of cytochrome c in the presence and absence of pyridine nucleotides. On the basis of these studies, we propose a model in which reduced FAD binds to SMOB in equilibrium between an unreactive, sequestered state (S state) and more reactive, transfer state (T state). The dissociation of NAD(+) after the hydride-transfer reaction transiently populates the T state, promoting the transfer of FADhq to NSMOA. The binding of pyridine nucleotides to SMOB-FADhq shifts the FADhq-binding equilibrium from the T state to the S state. Additionally, the 2.2 Å crystal structure of SMOB-FADox reported in this work is discussed in light of the pyridine nucleotide-gated flavin-transfer and electron-transfer reactions.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, San Francisco State University , San Francisco, California, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Styrene monooxygenase component 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
190Pseudomonas sp. Y2Mutation(s): 2 
Gene Names: styB
UniProt
Find proteins for O33495 (Pseudomonas sp. Y2)
Explore O33495 
Go to UniProtKB:  O33495
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO33495
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
EA [auth I]
GA [auth J]
KA [auth K]
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
KA [auth K],
LA [auth L],
M [auth A],
P [auth B],
R [auth C],
T [auth D],
X [auth E],
Z [auth F]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
JA [auth J],
V [auth D],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NO3
Query on NO3

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
FA [auth I]
HA [auth J]
IA [auth J]
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
IA [auth J],
MA [auth L],
N [auth A],
O [auth A],
Q [auth B],
S [auth C],
U [auth D],
Y [auth E]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.031α = 90
b = 130.031β = 90
c = 95.27γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description