7RAB

Crystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in a cubic lattice


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis.

Paavola, J.L.Battistin, U.Ogata, C.M.Georgiadis, M.M.

(2021) Acta Crystallogr D Struct Biol 77: 1336-1345

  • DOI: https://doi.org/10.1107/S205979832100944X
  • Primary Citation of Related Structures:  
    7RAB, 7RAC

  • PubMed Abstract: 

    Multicopper oxidases (MCOs) represent a diverse family of enzymes that catalyze the oxidation of either an organic or a metal substrate with concomitant reduction of dioxygen to water. These enzymes contain variable numbers of cupredoxin domains, two, three or six per subunit, and rely on four copper ions, a single type I copper and three additional copper ions organized in a trinuclear cluster (TNC), with one type II and two type III copper ions, to catalyze the reaction. Here, two crystal structures and the enzymatic characterization of Marinithermus hydrothermalis MCO, a two-domain enzyme, are reported. This enzyme decolorizes Congo Red dye at 70°C in the presence of high halide concentrations and may therefore be useful in the detoxification of industrial waste that contains dyes. In two distinct crystal structures, MhMCO forms the trimers seen in other two-domain MCOs, but differs from these enzymes in that four trimers interact to create a dodecamer. This dodecamer of MhMCO forms a closed ball-like structure and has implications for the sequestration of bound divalent metal ions as well as substrate accessibility. In each subunit of the dodecameric structures, a Trp residue, Trp351, located between the type I and TNC sites exists in two distinct conformations, consistent with a potential role in facilitating electron transfer in the enzyme.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
multicopper oxidase
A, B, C, D, E
A, B, C, D, E, F, G, H
348Marinithermus hydrothermalisMutation(s): 0 
Gene Names: Marky_0543
EC: 1.10.3.2
UniProt
Find proteins for F2NNS0 (Marinithermus hydrothermalis (strain DSM 14884 / JCM 11576 / T1))
Explore F2NNS0 
Go to UniProtKB:  F2NNS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2NNS0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
DA [auth H]
EA [auth H]
I [auth A]
AA [auth G],
BA [auth G],
DA [auth H],
EA [auth H],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
U [auth E],
V [auth E],
X [auth F],
Y [auth F]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
K [auth A]
N [auth B]
Q [auth C]
CA [auth G],
FA [auth H],
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.241α = 90
b = 224.241β = 90
c = 224.241γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description