4A68 | pdb_00004a68

Mutations in the neighbourhood of CotA-laccase trinuclear site: D116N mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.200 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4A68

This is version 1.3 of the entry. See complete history

Literature

The Role of Asp116 in the Reductive Cleavage of Dioxygen to Water in Cota Laccase: Assistance During the Proton Transfer Mechanism

Silva, C.S.Damas, J.M.Chen, Z.Brissos, V.Martins, L.O.Soares, C.M.Lindley, P.F.Bento, I.

(2012) Acta Crystallogr D Biol Crystallogr 68: 186

  • DOI: https://doi.org/10.1107/S0907444911054503
  • Primary Citation Related Structures: 
    4A66, 4A67, 4A68

  • PubMed Abstract: 

    Multi-copper oxidases constitute a family of proteins that are capable of coupling the one-electron oxidation of four substrate equivalents to the four-electron reduction of dioxygen to two molecules of water. The main catalytic stages occurring during the process have already been identified, but several questions remain, including the nature of the protonation events that take place during the reductive cleavage of dioxygen to water. The presence of a structurally conserved acidic residue (Glu498 in CotA laccase from Bacillus subtilis) at the dioxygen-entrance channel has been reported to play a decisive role in the protonation mechanisms, channelling protons during the reduction process and stabilizing the site as a whole. A second acidic residue that is sequentially conserved in multi-copper oxidases and sited within the exit channel (Asp116 in CotA) has also been identified as being important in the protonation process. In this study, CotA laccase has been used as a model system to assess the role of Asp116 in the reduction process of dioxygen to water. The crystal structures of three distinct mutants, D116E, D116N and D116A, produced by site-saturation mutagenesis have been determined. In addition, theoretical calculations have provided further support for a role of this residue in the protonation events.


  • Organizational Affiliation
    • Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da Republica, 2780-157 Oeiras, Portugal.

Macromolecule Content 

  • Total Structure Weight: 59.35 kDa 
  • Atom Count: 4,542 
  • Modeled Residue Count: 502 
  • Deposited Residue Count: 513 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SPORE COAT PROTEIN A513Bacillus subtilisMutation(s): 1 
EC: 1.10.3.2 (PDB Primary Data), 1.3.3.5 (UniProt)
UniProt
Find proteins for P07788 (Bacillus subtilis (strain 168))
Explore P07788 
Go to UniProtKB:  P07788
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07788
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
H [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
PER

Query on PER



Download:Ideal Coordinates CCD File
G [auth A]PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
OH

Query on OH



Download:Ideal Coordinates CCD File
F [auth A]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.200 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.548α = 90
b = 101.548β = 90
c = 136.717γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Other
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary