Crystal structure of Laccase from Thermus thermophilus HB27

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

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X-Ray-Induced Catalytic Active-Site Reduction of a Multicopper Oxidase: Structural Insights Into the Proton-Relay Mechanism and O2-Reduction States.

Serrano-Posada, H.Centeno-Leija, S.Rojas-Trejo, S.P.Rodriguez-Almazan, C.Stojanoff, V.Rudino-Pinera, E.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2396

  • DOI: https://doi.org/10.1107/S1399004715018714
  • Primary Citation of Related Structures:  
    2XU9, 2XUW, 2XVB, 2YAE, 2YAF, 2YAH, 2YAM, 2YAO, 2YAP, 2YAQ, 2YAR, 4AI7

  • PubMed Abstract: 

    During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O2 to 2H2O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase (Tth-MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth-MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O2 reduction was found in a double conformation: Glu451a (∼7 Å from the TNC) and Glu451b (∼4.5 Å from the TNC). A positive peak of electron density above 3.5σ in an Fo - Fc map for Glu451a O(ℇ2) indicates the presence of a carboxyl functional group at the side chain, while its significant absence in Glu451b strongly suggests a carboxylate functional group. In contrast, for apo Tth-MCO and in Hg-bound structures neither the positive peak nor double conformations were observed. Together, these observations provide the first structural evidence for a proton-relay mechanism in the MCO family and also support previous studies indicating that Asp106 does not provide protons for this mechanism. In addition, eight composite structures (Tth-MCO-C1-8) with different X-ray-absorbed doses allowed the observation of different O2-reduction states, and a total depletion of T2Cu at doses higher than 0.2 MGy showed the high susceptibility of this Cu atom to radiation damage, highlighting the importance of taking radiation effects into account in biochemical interpretations of an MCO structure.

  • Organizational Affiliation

    Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, 62210 Cuernavaca, MOR, Mexico.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LACCASE439Thermus thermophilus HB27Mutation(s): 1 
Find proteins for Q72HW2 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72HW2 
Go to UniProtKB:  Q72HW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72HW2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MRD

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth A],
T [auth A]
C6 H14 O2
Query on MPD

Download Ideal Coordinates CCD File 
E [auth A]
N [auth A]
O [auth A]
P [auth A]
Q [auth A]
E [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
S [auth A]
C6 H14 O2
Query on CU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
U [auth A]
Query on OH

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.578α = 90
b = 110.339β = 90
c = 96.317γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 1.2: 2015-12-16
    Changes: Database references
  • Version 1.3: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description