3PL8

Pyranose 2-oxidase H167A complex with 3-deoxy-3-fluoro-beta-D-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Regioselective control of Beta-d-glucose oxidation by pyranose 2-oxidase is intimately coupled to conformational degeneracy

Tan, T.C.Haltrich, D.Divne, C.

(2011) J Mol Biol 409: 588-600

  • DOI: 10.1016/j.jmb.2011.04.019
  • Primary Citation of Related Structures:  
    3PL8

  • PubMed Abstract: 
  • Trametes multicolor pyranose 2-oxidase (P2O) is a flavoprotein oxidase that oxidizes d-glucose at C2 to 2-keto-d-glucose by a highly regioselective mechanism. In this work, fluorinated sugar substrates were used as mechanistic probes to investigate t ...

    Trametes multicolor pyranose 2-oxidase (P2O) is a flavoprotein oxidase that oxidizes d-glucose at C2 to 2-keto-d-glucose by a highly regioselective mechanism. In this work, fluorinated sugar substrates were used as mechanistic probes to investigate the basis of regioselectivity in P2O. Although frequently used to study the mechanisms of glycoside hydrolases, our work provides the first example of applying these probes to sugar oxidoreductases. Our previous structure of the P2O mutant H167A in complex with the slow substrate 2-deoxy-2-fluoro-d-glucose showed a substrate-binding mode compatible with oxidation at C3. To accommodate the sugar, a gating segment, (454)FSY(456), in the substrate recognition loop partly unfolded to create a spacious and more polar active site that is distinct from the closed state of P2O. The crystal structure presented here shows that the preferred C2 oxidation where an ordered complex of P2O H167A with 3-deoxy-3-fluoro-d-glucose at 1.35 Å resolution was successfully trapped. In this semi-open C2-oxidation complex, the substrate recognition loop tightens to form an optimized substrate complex stabilized by interactions between Asp452 and glucose O4, as well as Tyr456 and the glucose O6 group, interactions that are not possible when glucose is positioned for oxidation at C3. The different conformations of the (454)FSY(456) gating segment in the semi-open and closed states induce backbone and side-chain movements of Thr169 and Asp452 that add further differential stabilization to the individual states. We expect the semi-open state (C2-oxidation state) and closed state to be good approximations of the active-site structure during the reductive half-reaction (sugar oxidation) and oxidative half-reaction (O(2) reduction).


    Organizational Affiliation

    Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, SE-17177 Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyranose 2-oxidaseA623Trametes ochraceaMutation(s): 1 
Gene Names: p2o
EC: 1.1.3.10
Find proteins for Q7ZA32 (Trametes ochracea)
Explore Q7ZA32 
Go to UniProtKB:  Q7ZA32
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
G3F
Query on G3F

Download CCD File 
A
3-deoxy-3-fluoro-beta-D-glucopyranose
C6 H11 F O5
BUMRBAMACDBPKO-AIECOIEWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.55α = 90
b = 101.55β = 90
c = 127.16γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-11-14 
  • Released Date: 2011-04-27 
  • Deposition Author(s): Tan, T.C., Divne, C.

Revision History 

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-24
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Data collection, Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations