5TKI

Neurospora crassa polysaccharide monooxygenase 2 resting state joint X-ray/neutron refinement


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase.

O'Dell, W.B.Agarwal, P.K.Meilleur, F.

(2017) Angew Chem Int Ed Engl 56: 767-770

  • DOI: https://doi.org/10.1002/anie.201610502
  • Primary Citation of Related Structures:  
    5TKG, 5TKH, 5TKI

  • PubMed Abstract: 

    Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. We have determined high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed "pre-bound" molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygen activation. These results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme-substrate complex.


  • Organizational Affiliation

    Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lytic polysaccharide monooxygenase
A, B
223Neurospora crassaMutation(s): 0 
Gene Names: G15G9.090GE21DRAFT_7469
EC: 1.14.99.56
UniProt
Find proteins for Q1K8B6 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore Q1K8B6 
Go to UniProtKB:  Q1K8B6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1K8B6
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 1 21 1
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.12α = 90
b = 42.23β = 98.33
c = 70.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
LAUEGENdata reduction
LSCALEdata scaling
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1069091

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary