8P9V | pdb_00008p9v

Crystal Structure of Two-Domain Laccase mutant M199G/R240H/D268N from Streptomyces griseoflavus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8P9V

This is version 1.0 of the entry. See complete history

Literature

Structural Insight into the Amino Acid Environment of the Two-Domain Laccase's Trinuclear Copper Cluster.

Kolyadenko, I.Tishchenko, S.Gabdulkhakov, A.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms241511909
  • Primary Citation Related Structures: 
    8P9U, 8P9V

  • PubMed Abstract: 

    Laccases are industrially relevant enzymes. However, their range of applications is limited by their functioning and stability. Most of the currently known laccases function in acidic conditions at temperatures below 60 °C, but two-domain laccases (2D) oxidize some substrates in alkaline conditions and above 70 °C. In this study, we aim to establish the structural factors affecting the alkaline activity of the 2D laccase from Streptomyces griseoflavus (SgfSL). The range of methods used allowed us to show that the alkaline activity of SgfSL is influenced by the polar residues located close to the trinuclear center (TNC). Structural and functional studies of the SgfSL mutants Met199Ala/Asp268Asn and Met199Gly/Asp268Asn revealed that the substitution Asp268Asn (11 Å from the TNC) affects the orientation of the Asn261 (the second coordination sphere of the TNC), resulting in hydrogen-bond-network reorganization, which leads to a change in the SgfSL-activity pH profile. The combination of the Met199Gly/Arg240His and Asp268Asn substitutions increased the efficiency (k cat /K M ) of the 2,6-DMP oxidation by 34-fold compared with the SgfSL. Our results extend the knowledge about the structure and functioning of 2D laccases' TNC active sites and open up new possibilities for the directed engineering of laccases.


  • Organizational Affiliation
    • Institute of Protein Research RAS, 142290 Pushchino, Russia.

Macromolecule Content 

  • Total Structure Weight: 182.85 kDa 
  • Atom Count: 12,923 
  • Modeled Residue Count: 1,659 
  • Deposited Residue Count: 1,668 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Two-domain laccase
A, B, C, D, E
A, B, C, D, E, F
278Streptomyces griseoflavusMutation(s): 3 
EC: 1.10.3.2
UniProt
Find proteins for A0A0M4FJ81 (Streptomyces griseoflavus)
Explore A0A0M4FJ81 
Go to UniProtKB:  A0A0M4FJ81
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4FJ81
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU
(Subject of Investigation/LOI)

Query on CU



Download:Ideal Coordinates CCD File
AA [auth E]
BA [auth E]
CA [auth E]
FA [auth F]
GA [auth F]
AA [auth E],
BA [auth E],
CA [auth E],
FA [auth F],
GA [auth F],
HA [auth F],
I [auth A],
IA [auth F],
J [auth A],
K [auth A],
L [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth C],
S [auth C],
T [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
OXY
(Subject of Investigation/LOI)

Query on OXY



Download:Ideal Coordinates CCD File
DA [auth F],
EA [auth F],
G [auth A],
H [auth A]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
PER
(Subject of Investigation/LOI)

Query on PER



Download:Ideal Coordinates CCD File
U [auth D]PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.37α = 90
b = 93.92β = 91.1
c = 119.591γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release