5KQ6

Crystal structure of the A359D variant of catalase-peroxidase from B. pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine.

Machuqueiro, M.Victor, B.Switala, J.Villanueva, J.Rovira, C.Fita, I.Loewen, P.C.

(2017) Biochemistry 56: 2271-2281

  • DOI: 10.1021/acs.biochem.6b01276
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The unusual Met-Tyr-Trp adduct composed of cross-linked side chains along with an associated mobile Arg is essential for catalase activity in catalase-peroxidases. In addition, acidic residues in the entrance channel, in particular an Asp and a Glu ∼ ...

    The unusual Met-Tyr-Trp adduct composed of cross-linked side chains along with an associated mobile Arg is essential for catalase activity in catalase-peroxidases. In addition, acidic residues in the entrance channel, in particular an Asp and a Glu ∼7 and ∼15 Å, respectively, from the heme, significantly enhance catalase activity. The mechanism by which these channel carboxylates influence catalase activity is the focus of this work. Seventeen new variants with fewer and additional acidic residues have been constructed and characterized structurally and for enzymatic activity, revealing that their effect on activity is roughly inversely proportional to their distance from the heme and adduct, suggesting that the electrostatic potential of the heme cavity may be affected. A discrete group of protonable residues are contained within a 15 Å sphere surrounding the heme iron, and a computational analysis reveals that the pK a of the distal His 112 , alone, is modulated within the pH range of catalase activity by the remote acidic residues in a pattern consistent with its protonated form having a key role in the catalase reaction cycle. The electrostatic potential also impacts the catalatic reaction through its influence on the charged status of the Met-Tyr-Trp adduct.


    Organizational Affiliation

    Department of Microbiology, University of Manitoba , Winnipeg, MB R3T 2N2, Canada.,Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa, Portugal.,Institut de Biología Molecular de Barcelona (CSIC), Parc Científic de Barcelona , Baldiri i Reixac 10-12, 08028 Barcelona, Spain.,Departament de Química Organica and Institut de Química Teòrica i Computacional (IQTCUB), Universtat de Barcelona , Martí i Franquès 1, 08028 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catalase-peroxidase
A, B
728Burkholderia pseudomallei (strain 1710b)Mutation(s): 1 
Gene Names: katG
EC: 1.11.1.21
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JNW6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TOX
Query on TOX
A, B
L-PEPTIDE LINKINGC11 H12 N2 O4TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.577α = 90.00
b = 115.791β = 90.00
c = 174.726γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-07-05 
  • Released Date: 2017-04-26 
  • Deposition Author(s): Loewen, P.C.

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)CanadaD9600

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence