PDBsum entry 2yam

Oxidoreductase

PDB id: 2yam

Contents

Protein chain

439 a.a.

Ligands

MPD ×7

MRD ×9

_OH

Metals

_CU ×3

Waters ×498

PDB id:

2yam

Name:

Oxidoreductase

Title:

X-ray induced reduction of laccase from thermus thermophilus hb27 (37. 5-50.0 percent dose)

Structure:

Laccase. Chain: a. Fragment: mature form, residues 24-462. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.80Å R-factor: 0.148 R-free: 0.172

Authors:

H.Serrano-Posada,E.Rudino-Pinera

Key ref:

H.Serrano-Posada et al. (2015). X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states. Acta Crystallogr D Biol Crystallogr, 71, 2396-2411. PubMed id: 26627648 DOI: 10.1107/S1399004715018714

Date:

23-Feb-11 Release date: 29-Feb-12

Protein chain

Q72HW2  (Q72HW2_THET2) -  Laccase from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 462 a.a.

Struc: 440 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.10.3.2 - laccase.
• Reaction: 4 hydroquinone + O2 = 4 benzosemiquinone + 2 H2O
• Cofactor: Cu cation

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1107/S1399004715018714

Acta Crystallogr D Biol Crystallogr 71:2396-2411 (2015)

PubMed id: 26627648

X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states.

H.Serrano-Posada, S.Centeno-Leija, S.P.Rojas-Trejo, C.Rodríguez-Almazán, V.Stojanoff, E.Rudiño-Piñera.

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.