5O4Q

Crystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase from Streptomyces griseoflavus with 0.25 mM copper sulfate on growth medium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Incorporation of Copper Ions into T2/T3 Centers of Two-Domain Laccases.

Gabdulkhakov, A.G.Kostareva, O.S.Kolyadenko, I.A.Mikhaylina, A.O.Trubitsina, L.I.Tishchenko, S.V.

(2018) Mol Biol (Mosk) 52: 29-35

  • DOI: https://doi.org/10.7868/S0026898418010056
  • Primary Citation of Related Structures:  
    5O3K, 5O4I, 5O4Q

  • PubMed Abstract: 

    Laccase belongs to the family of copper-containing oxidases. A study was made of the mechanism that sustains the incorporation of copper ions into the T2/T3 centers of recombinant two-domain laccase Streptomyces griseoflavus Ac-993. The occupancy of the T3 center by copper ions was found to increase with an increasing copper content in the culture medium and after dialysis of the protein preparation against a copper sulfate-containing buffer. The T2 center was filled only when overproducer strain cells were grown at a higher copper concentration in the medium. Two-domain laccases were assumed to possess a channel that serves to deliver copper ions to the T3 center during the formation of the three-dimensional laccase conformation and dialysis of the protein preparation. A narrower channel leads to the T2 center in two-domain laccases compared with three-domain ones, rendering the center less accessible for copper atoms. The incorporation of copper ions into the T2 center of two-domain laccases is likely to occur in the course of their biosynthesis or the formation of a functional trimer.


  • Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Two-domain laccase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
322Streptomyces 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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
NA [auth J],
O [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4
Query on SO4

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QA [auth K]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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S [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

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BA [auth F]
CA [auth F]
DA [auth G]
EA [auth G]
FA [auth H]
BA [auth F],
CA [auth F],
DA [auth G],
EA [auth G],
FA [auth H],
GA [auth H],
IA [auth I],
JA [auth I],
KA [auth J],
LA [auth J],
M [auth A],
N [auth A],
OA [auth K],
P [auth B],
PA [auth K],
Q [auth B],
RA [auth L],
SA [auth L],
T [auth C],
U [auth C],
V [auth D],
W [auth D],
Y [auth E],
Z [auth E]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
FMT
Query on FMT

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X [auth D]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
AZI
Query on AZI

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AA [auth E],
HA [auth H],
MA [auth J],
R [auth B]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.841α = 90.04
b = 94.85β = 90.29
c = 116.614γ = 91.49
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description