6FYG

The crystal structure of EncM V135T mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enzymatic control of dioxygen binding and functionalization of the flavin cofactor.

Saleem-Batcha, R.Stull, F.Sanders, J.N.Moore, B.S.Palfey, B.A.Houk, K.N.Teufel, R.

(2018) Proc Natl Acad Sci U S A 115: 4909-4914

  • DOI: 10.1073/pnas.1801189115
  • Primary Citation of Related Structures:  
    6FOQ, 6FOW, 6FP3, 6FY8, 6FY9, 6FYA, 6FYB, 6FYC, 6FYD, 6FYE, 6FYF, 6FYG

  • PubMed Abstract: 
  • The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O 2 ) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O 2 , as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates ...

    The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O 2 ) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O 2 , as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates. Here we employ O 2 -pressurized X-ray crystallography and quantum mechanical calculations to reveal how the precise positioning of O 2 within a flavoenzyme's active site enables the regiospecific formation of a covalent flavin-oxygen adduct and oxygenating species (i.e., the flavin-N5-oxide) by mimicking a critical transition state. This study unambiguously demonstrates how enzymes may control the O 2 functionalization of an organic cofactor as prerequisite for oxidative catalysis. Our work thus illustrates how O 2 reactivity can be harnessed in an enzymatic environment and provides crucial knowledge for future rational design of O 2 -reactive enzymes.


    Organizational Affiliation

    Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative FAD-dependent oxygenase EncMA, B, C, D464Streptomyces maritimusMutation(s): 1 
Gene Names: encM
UniProt
Find proteins for Q9KHK2 (Streptomyces maritimus)
Explore Q9KHK2 
Go to UniProtKB:  Q9KHK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KHK2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.806α = 90
b = 174.229β = 90
c = 131.773γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyTE931/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references