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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 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

    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. Electronic address: jsunkim@chonnam.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Baeyer-Villiger monooxygenaseAB544Parvibaculum lavamentivorans DS-1Mutation(s): 0 
Gene Names: Plav_1781
EC: 1.14.13
Find proteins for A7HU16 (Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966))
Explore A7HU16 
Go to UniProtKB:  A7HU16
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references