2XLT

Joint-functions of protein residues and NADP(H) in oxygen-activation by flavin-containing monooxygenase: complex with 3-Acetylpyridine adenine dinucleotide phosphate (APADP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Joint functions of protein residues and NADP(H) in oxygen activation by flavin-containing monooxygenase.

Orru, R.Pazmino, D.E.Fraaije, M.W.Mattevi, A.

(2010) J Biol Chem 285: 35021-35028

  • DOI: https://doi.org/10.1074/jbc.M110.161372
  • Primary Citation of Related Structures:  
    2XLP, 2XLR, 2XLS, 2XLT, 2XLU

  • PubMed Abstract: 

    The reactivity of flavoenzymes with dioxygen is at the heart of a number of biochemical reactions with far reaching implications for cell physiology and pathology. Flavin-containing monooxygenases are an attractive model system to study flavin-mediated oxygenation. In these enzymes, the NADP(H) cofactor is essential for stabilizing the flavin intermediate, which activates dioxygen and makes it ready to react with the substrate undergoing oxygenation. Our studies combine site-directed mutagenesis with the usage of NADP(+) analogues to dissect the specific roles of the cofactors and surrounding protein matrix. The highlight of this "double-engineering" approach is that subtle alterations in the hydrogen bonding and stereochemical environment can drastically alter the efficiency and outcome of the reaction with oxygen. This is illustrated by the seemingly marginal replacement of an Asn to Ser in the oxygen-reacting site, which inactivates the enzyme by effectively converting it into an oxidase. These data rationalize the effect of mutations that cause enzyme deficiency in patients affected by the fish odor syndrome. A crucial role of NADP(+) in the oxygenation reaction is to shield the reacting flavin N5 atom by H-bond interactions. A Tyr residue functions as backdoor that stabilizes this crucial binding conformation of the nicotinamide cofactor. A general concept emerging from this analysis is that the two alternative pathways of flavoprotein-oxygen reactivity (oxidation versus monooxygenation) are predicted to have very similar activation barriers. The necessity of fine tuning the hydrogen-bonding, electrostatics, and accessibility of the flavin will represent a challenge for the design and development of oxidases and monoxygenases for biotechnological applications.


  • Organizational Affiliation

    Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FLAVIN-CONTAINING MONOOXYGENASE
A, B, C, D
461Methylophaga aminisulfidivoransMutation(s): 0 
EC: 1.14.13.8 (PDB Primary Data), 1.14.13.148 (UniProt)
UniProt
Find proteins for Q83XK4 (Methylophaga aminisulfidivorans)
Explore Q83XK4 
Go to UniProtKB:  Q83XK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83XK4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
S [auth C],
X [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NA0
Query on NA0

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
T [auth C],
Y [auth D]
3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE PHOSPHATE
C22 H29 N6 O17 P3
CWZSJEPJRFQEBR-SIEFPTHMSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
K [auth A],
R [auth B],
Z [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
G [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
U [auth C],
V [auth C],
W [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.748α = 90
b = 219.748β = 90
c = 130.624γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Database references, Version format compliance
  • Version 1.2: 2019-02-27
    Changes: Data collection, Database references, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description