1LY8

The crystal structure of a mutant enzyme of Coprinus cinereus peroxidase provides an understanding of its increased thermostability and insight into modelling of protein structures


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view detailsBest fitted MANClick on this verticalbar to view detailsBest fitted BMAClick on this verticalbar to view details

This is version 1.7 of the entry. See complete history


Literature

The structure of a mutant enzyme of Coprinus cinereus peroxidase provides an understanding of its increased thermostability.

Houborg, K.Harris, P.Poulsen, J.C.Schneider, P.Svendsen, A.Larsen, S.

(2003) Acta Crystallogr D Biol Crystallogr 59: 997-1003

  • DOI: https://doi.org/10.1107/s0907444903006784
  • Primary Citation of Related Structures:  
    1LY8

  • PubMed Abstract: 

    Seven amino-acid substitutions introduced into the 343 amino-acid-long sequence of Coprinus cinereus peroxidase (CiP) led to a mutant enzyme (TS-rCiP) which is more stable than the native enzyme at higher temperature, pH and hydrogen peroxide concentrations. It is therefore more suitable for industrial applications. A structure determination was conducted on a deglycosylated but still active form of TS-rCiP based on X-ray diffraction data to 2.05 A resolution measured on a crystal cooled to 100 K and refined to R = 0.202 and R(free) = 0.249. The increased stability of the TS-rCiP enzyme can be understood from the structural changes of the TS-rCiP structure revealed by a comparative analysis with other known CiP structures. One of the more significant changes caused by three of the substitutions, I49S, V53A and T121A, is the conversion of a hydrophobic pocket into a hydrophilic pocket with associated changes in the water structure and the hydrogen-bonding interactions. The E239G substitution, which gives rise to increased thermostability at high pH, creates changes in the water structure and in the orientation of a phenylalanine (Phe236) in its vicinity. The three substitutions M166F, M242 and Y242F introduced to increase the oxidative stability do not introduce any structural changes.


  • Organizational Affiliation

    Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxidase
A, B
343Coprinopsis cinereaMutation(s): 7 
Gene Names: CIP1
EC: 1.11.1.7
UniProt
Find proteins for P28314 (Coprinopsis cinerea)
Explore P28314 
Go to UniProtKB:  P28314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28314
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
H [auth A],
R [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG
Query on NAG

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

Download Ideal Coordinates CCD File 
E [auth A],
O [auth B]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA
Query on BMA

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

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
P [auth B],
Q [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.49α = 90
b = 114.86β = 90
c = 73.61γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view detailsBest fitted MANClick on this verticalbar to view detailsBest fitted BMAClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2018-03-07
    Changes: Data collection
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2021-10-27
    Changes: Database references, Structure summary
  • Version 1.7: 2024-10-09
    Changes: Data collection, Structure summary