6K9O

Crystal Structure Analysis of Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.121 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2DFC 4KHI 4kH9


Literature

Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography.

Li, Z.Zhang, X.Li, C.Kovalevsky, A.Wan, Q.

(2020) Protein J 39: 671-680

  • DOI: https://doi.org/10.1007/s10930-020-09938-5
  • Primary Citation of Related Structures:  
    6JUG, 6JWB, 6K9O, 6K9R, 6K9W, 6KW9, 6KWC, 6KWD, 6KWF, 6KWG

  • PubMed Abstract: 

    XynII is a family 11 glycoside hydrolase that uses the retaining mechanism for catalysis. In the active site, E177 works as the acid/base and E86 works as the nucleophile. Mutating an uncharged residue (N44) to an acidic residue (D) near E177 decreases the enzyme's optimal pH by ~ 1.0 unit. D44 was previously suggested to be a second proton carrier for catalysis. To test this hypothesis, we abolished the activity of E177 by mutating it to be Q, and mutated N44 to be D or E. These double mutants have dramatically decreased activities. Our high-resolution crystallographic structures and the microscopic pK a calculations show that D44 has similar position and pK a value during catalysis, indicating that D44 changes electrostatics around E177, which makes it prone to rotate as the acid/base in acidic conditions, thus decreases the pH optimum. Our results could be helpful to design enzymes with different pH optimum.


  • Organizational Affiliation

    College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase 2189Trichoderma reesei RUT C-30Mutation(s): 1 
Gene Names: xyn2
EC: 3.2.1.8
UniProt
Find proteins for P36217 (Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30))
Explore P36217 
Go to UniProtKB:  P36217
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36217
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.96α = 90
b = 59.334β = 90
c = 69.845γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-06-17 
  • Deposition Author(s): Li, C., Wan, Q.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670790

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description