6JDK

Crystal structure of Baeyer-Villiger monooxygenase from Parvibaculum lavamentivorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for the selective addition of an oxygen atom to cyclic ketones by Baeyer-Villiger monooxygenase from Parvibaculum lavamentivorans.

Nguyen, T.D.Choi, G.E.Gu, D.H.Seo, P.W.Kim, J.W.Park, J.B.Kim, J.S.

(2019) Biochem Biophys Res Commun 512: 564-570

  • DOI: https://doi.org/10.1016/j.bbrc.2019.03.114
  • Primary Citation of Related Structures:  
    6JDK

  • PubMed Abstract: 

    Baeyer-Villiger monooxygenase (BVMO) catalyzes insertion of an oxygen atom into aliphatic or cyclic ketones with high regioselectivity. The BVMOs from Parvibaculum lavamentivorans (BVMO Parvi ) and Oceanicola batsensis (BVMO Ocean ) are interesting because of their homologies, with >40% sequence identity, and reaction with the same cyclic ketones with a methyl moiety to give different products. The revealed BVMO Parvi structure shows that BVMO Parvi forms a two-domain structure like other BVMOs. It has two inserted residues, compared with BVMO Ocean , that form a bulge near the bound flavin adenine dinucleotide in the active site. Furthermore, this bulge is linked to a nearby α-helix via a disulfide bond, probably restricting access of the bulky methyl group of the substrate to this bulge. Another sequence motif at the entrance of the active site (Ala-Ser in BVMO Parvi and Ser-Thr in BVMO Ocean ) allows a large volume in BVMO Parvi . These minute differences may discriminate a substrate orientation in both BVMOs from the initial substrate binding pocket to the final oxygenation site, resulting in the inserted oxygen atom being in different positions of the same substrate.


  • Organizational Affiliation

    Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Baeyer-Villiger monooxygenase
A, B
544Parvibaculum lavamentivorans DS-1Mutation(s): 0 
Gene Names: Plav_1781
EC: 1.14.13
UniProt
Find proteins for A7HU16 (Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966))
Explore A7HU16 
Go to UniProtKB:  A7HU16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7HU16
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.831α = 90
b = 55.049β = 95.25
c = 118.099γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary