7VN0

CATPO mutant - T188A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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


Literature

Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase.

Yuzugullu Karakus, Y.Goc, G.Zengin Karatas, M.Balci Unver, S.Yorke, B.A.Pearson, A.R.

(2024) Acta Crystallogr D Struct Biol 80: 101-112

  • DOI: https://doi.org/10.1107/S2059798323011063
  • Primary Citation of Related Structures:  
    5YEM, 7VN0, 7WCA

  • PubMed Abstract: 

    Catalase is an antioxidant enzyme that breaks down hydrogen peroxide (H 2 O 2 ) into molecular oxygen and water. In all monofunctional catalases the pathway that H 2 O 2 takes to the catalytic centre is via the `main channel'. However, the structure of this channel differs in large-subunit and small-subunit catalases. In large-subunit catalases the channel is 15 Å longer and consists of two distinct parts, including a hydrophobic lower region near the heme and a hydrophilic upper region where multiple H 2 O 2 routes are possible. Conserved glutamic acid and threonine residues are located near the intersection of these two regions. Mutations of these two residues in the Scytalidium thermophilum catalase had no significant effect on catalase activity. However, the secondary phenol oxidase activity was markedly altered, with k cat and k cat /K m values that were significantly increased in the five variants E484A, E484I, T188D, T188I and T188F. These variants also showed a lower affinity for inhibitors of oxidase activity than the wild-type enzyme and a higher affinity for phenolic substrates. Oxidation of heme b to heme d did not occur in most of the studied variants. Structural changes in solvent-chain integrity and channel architecture were also observed. In summary, modification of the main-channel gate glutamic acid and threonine residues has a greater influence on the secondary activity of the catalase enzyme, and the oxidation of heme b to heme d is predominantly inhibited by their conversion to aliphatic and aromatic residues.


  • Organizational Affiliation

    Department of Biology, Kocaeli University, Kabaoglu, Kocaeli, Izmit 41001, Türkiye.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase
A, B, C, D
720Mycothermus thermophilusMutation(s): 1 
EC: 1.11.1.6
UniProt
Find proteins for M4GGR5 (Mycothermus thermophilus)
Explore M4GGR5 
Go to UniProtKB:  M4GGR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM4GGR5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HDD (Subject of Investigation/LOI)
Query on HDD

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
P [auth D]
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
C34 H32 Fe N4 O5
UMGOPAWIGKFTRK-QQDQPIDJSA-N
ALA
Query on ALA

Download Ideal Coordinates CCD File 
O [auth D]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.944α = 90
b = 120.786β = 101.9
c = 184.747γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government113Z744

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-02-14
    Changes: Database references