3X2O

Neutron and X-ray joint refined structure of PcCel45A apo form at 298K.


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

"Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography.

Nakamura, A.Ishida, T.Kusaka, K.Yamada, T.Fushinobu, S.Tanaka, I.Kaneko, S.Ohta, K.Tanaka, H.Inaka, K.Higuchi, Y.Niimura, N.Samejima, M.Igarashi, K.

(2015) Sci Adv 1: e1500263-e1500263

  • DOI: 10.1126/sciadv.1500263
  • Primary Citation of Related Structures:  
    3X2G, 3X2H, 3X2I, 3X2J, 3X2K, 3X2L, 3X2M, 3X2N, 3X2O, 3X2P, 4ZM7

  • PubMed Abstract: 
  • Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium ...

    Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.


    Organizational Affiliation

    Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoglucanase V-like proteinA180Phanerodontia chrysosporiumMutation(s): 0 
Gene Names: egvPcCel45A
UniProt
Find proteins for B3Y002 (Phanerodontia chrysosporium)
Explore B3Y002 
Go to UniProtKB:  B3Y002
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3Y002
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
41Q
Query on 41Q
A L-PEPTIDE LINKINGC4 H8 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.152α = 90
b = 59.067β = 90
c = 64.285γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
STARGAZERdata reduction
STARGAZERdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection
  • Version 1.2: 2018-05-16
    Changes: Data collection
  • Version 1.3: 2019-12-18
    Changes: Data collection, Database references, Derived calculations