1JKU

Crystal Structure of Manganese Catalase from Lactobacillus plantarum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

Starting Model: other
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of manganese catalase from Lactobacillus plantarum.

Barynin, V.V.Whittaker, M.M.Antonyuk, S.V.Lamzin, V.S.Harrison, P.M.Artymiuk, P.J.Whittaker, J.W.

(2001) Structure 9: 725-738

  • DOI: https://doi.org/10.1016/s0969-2126(01)00628-1
  • Primary Citation of Related Structures:  
    1JKU, 1JKV

  • PubMed Abstract: 

    Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and the other, a structurally distinct family containing nonheme manganese. We have solved the structure of the mesophilic manganese catalase from Lactobacillus plantarum and its azide-inhibited complex. The crystal structure of the native enzyme has been solved at 1.8 A resolution by molecular replacement, and the azide complex of the native protein has been solved at 1.4 A resolution. The hexameric structure of the holoenzyme is stabilized by extensive intersubunit contacts, including a beta zipper and a structural calcium ion crosslinking neighboring subunits. Each subunit contains a dimanganese active site, accessed by a single substrate channel lined by charged residues. The manganese ions are linked by a mu1,3-bridging glutamate carboxylate and two mu-bridging solvent oxygens that electronically couple the metal centers. The active site region includes two residues (Arg147 and Glu178) that appear to be unique to the Lactobacillus plantarum catalase. A comparison of L. plantarum and T. thermophilus catalase structures reveals the existence of two distinct structural classes, differing in monomer design and the organization of their active sites, within the manganese catalase family. These differences have important implications for catalysis and may reflect distinct biological functions for the two enzymes, with the L. plantarum enzyme serving as a catalase, while the T. thermophilus enzyme may function as a catalase/peroxidase.


  • Organizational Affiliation

    The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, United Kingdom. v.barynin@sheffield.ac.uk


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pseudocatalase
A, B, C, D, E
A, B, C, D, E, F
266Lactiplantibacillus plantarumMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for P60355 (Lactiplantibacillus plantarum)
Explore P60355 
Go to UniProtKB:  P60355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60355
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN3
Query on MN3

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
IA [auth E]
JA [auth E]
K [auth A]
CA [auth D],
DA [auth D],
IA [auth E],
JA [auth E],
K [auth A],
L [auth A],
OA [auth F],
PA [auth F],
Q [auth B],
R [auth B],
W [auth C],
X [auth C]
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth E]
G [auth A]
KA [auth F]
M [auth B]
S [auth C]
EA [auth E],
G [auth A],
KA [auth F],
M [auth B],
S [auth C],
Y [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
OH
Query on OH

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
FA [auth E]
GA [auth E]
H [auth A]
AA [auth D],
BA [auth D],
FA [auth E],
GA [auth E],
H [auth A],
HA [auth E],
I [auth A],
J [auth A],
LA [auth F],
MA [auth F],
N [auth B],
NA [auth F],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.72α = 90
b = 96.42β = 106.88
c = 106.69γ = 90
Software Package:
Software NamePurpose
DMmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description