1HGY

CEL6A D221A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

The Active Site of Cellobiohydrolase Cel6A from Trichoderma Reesei: The Roles of Aspartic Acids D221 and D175

Koivula, A.Ruohonen, L.Wohlfahrt, G.Reinikainen, T.Teeri, T.T.Piens, K.Claeyssens, M.Weber, M.Vasella, A.Becker, D.Sinnott, M.L.Zou, J.-Y.Kleywegt, G.J.Szardenings, M.Stahlberg, J.Jones, T.A.

(2002) J Am Chem Soc 124: 10015

  • DOI: https://doi.org/10.1021/ja012659q
  • Primary Citation of Related Structures:  
    1HGW, 1HGY

  • PubMed Abstract: 

    Trichoderma reesei cellobiohydrolase Cel6A is an inverting glycosidase. Structural studies have established that the tunnel-shaped active site of Cel6A contains two aspartic acids, D221 and D175, that are close to the glycosidic oxygen of the scissile bond and at hydrogen-bonding distance from each other. Here, site-directed mutagenesis, X-ray crystallography, and enzyme kinetic studies have been used to confirm the role of residue D221 as the catalytic acid. D175 is shown to affect protonation of D221 and to contribute to the electrostatic stabilization of the partial positive charge in the transition state. Structural and modeling studies suggest that the single-displacement mechanism of Cel6A may not directly involve a catalytic base. The value of (D2O)(V) of 1.16 +/- 0.14 for hydrolysis of cellotriose suggests that the large direct effect expected for proton transfer from the nucleophilic water through a water chain (Grotthus mechanism) is offset by an inverse effect arising from reversibly breaking the short, tight hydrogen bond between D221 and D175 before catalysis.


  • Organizational Affiliation

    VTT Biotechnology, P.O. Box 1500, FIN-02044 VTT, Espoo, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
A, B
365Trichoderma reeseiMutation(s): 1 
Gene Names: CBH2 (D221A)
EC: 3.2.1.91
UniProt
Find proteins for P07987 (Hypocrea jecorina)
Explore P07987 
Go to UniProtKB:  P07987
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07987
Glycosylation
Glycosylation Sites: 8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
N [auth B],
O [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLC
Query on GLC

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
BMA
Query on BMA

Download Ideal Coordinates CCD File 
J [auth A]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.6α = 76.3
b = 67.5β = 75.2
c = 53.8γ = 78.4
Software Package:
Software NamePurpose
CNSrefinement
MADNESSdata reduction
MADNESSdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-10-16
    Changes: Structure summary