4B7F

Structure of a liganded bacterial catalase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Structural and Dynamic Investigation of the Inhibition of Catalase by Nitric Oxide.

Candelaresi, M.Gumiero, A.Adamczyk, K.Robb, K.Bellota-Anton, C.Sangal, V.Munnoch, J.Greetham, G.M.Towrie, M.Hoskisson, P.A.Parker, A.W.Tucker, N.P.Walsh, M.A.Hunt, N.T.

(2013) Org.Biomol.Chem. 11: 7778

  • DOI: 10.1039/c3ob41977k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Determining the chemical and structural modifications occurring within a protein during fundamental processes such as ligand or substrate binding is essential to building up a complete picture of biological function. Currently, significant unanswered ...

    Determining the chemical and structural modifications occurring within a protein during fundamental processes such as ligand or substrate binding is essential to building up a complete picture of biological function. Currently, significant unanswered questions relate to the way in which protein structural dynamics fit within the structure-function relationship and to the functional role, if any, of bound water molecules in the active site. Addressing these questions requires a multidisciplinary approach and complementary experimental techniques that, in combination, enhance our understanding of the complexities of protein chemistry. We exemplify this philosophy by applying both physical and biological approaches to investigate the active site chemistry that contributes to the inhibition of the Corynebacterium glutamicum catalase enzyme by nitric oxide. Ultrafast two-dimensional infrared spectroscopy (2D-IR) experiments exploit the NO ligand as a local probe of the active site molecular environment and shows that catalase displays a dynamically-restricted, 'tight,' structure. X-ray crystallography studies of C. glutamicum catalase confirm the presence of a conserved chain of hydrogen-bonded bound water molecules that link the NO ligand and the protein scaffold. This combination of bound water and restricted dynamics stands in stark contrast to other haem proteins, such as myoglobin, that exhibit ligand transport functionality despite the presence of a similar distal architecture in close proximity to the ligand. We conclude not only that the bound water molecules in the catalase active site play an important role in molecular recognition of NO but also may be part of the mechanistic operation of this important enzyme.


    Organizational Affiliation

    Department of Physics, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK. neil.hunt@strath.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catalase
A, B, C, D
515Corynebacterium glutamicumMutation(s): 0 
Gene Names: cat
EC: 1.11.1.6
Find proteins for A0A0U4WRC5 (Corynebacterium glutamicum)
Go to UniProtKB:  A0A0U4WRC5
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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

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Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
D
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
NO
Query on NO

Download SDF File 
Download CCD File 
A, B, C, D
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B, C, D
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 151.510α = 90.00
b = 151.510β = 90.00
c = 156.620γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-20 
  • Released Date: 2013-08-28 
  • Deposition Author(s): Gumiero, A., Walsh, M.

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Database references
  • Version 1.2: 2019-04-24
    Type: Data collection, Database references, Other, Source and taxonomy, Structure summary