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 
  • R-Value Observed: 0.160 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1039/c3ob41977k
  • Primary Citation of Related Structures:  
    4B7F, 4B7G, 4B7H

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase
A, B, C, D
515Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: catAPT58_01635CS176_0252FM102_06680
EC: 1.11.1.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
Q [auth C],
V [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B],
T [auth C],
Z [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BTB
Query on BTB

Download Ideal Coordinates CCD File 
U [auth D]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
L [auth B]
N [auth B]
O [auth B]
R [auth C]
H [auth A],
L [auth B],
N [auth B],
O [auth B],
R [auth C],
W [auth D],
Y [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NO
Query on NO

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
S [auth C],
X [auth D]
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.51α = 90
b = 151.51β = 90
c = 156.62γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2014-04-23
    Changes: Database references
  • Version 1.2: 2019-04-24
    Changes: Data collection, Database references, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2019-07-10
    Changes: Data collection
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description