6ZIJ

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

PDB DOI: https://doi.org/10.2210/pdb6ZIJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces griseoflavus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-06-26 Released: 2021-05-05
Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, T.V., Kolyadenko, I.A.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.181
R-Value Work: 0.145
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The role of positive charged residue in the proton-transfer mechanism of two-domain laccase from Streptomyces griseoflavus Ac-993.

Gabdulkhakov, A., Kolyadenko, I., Oliveira, P., Tamagnini, P., Mikhaylina, A., Tishchenko, S.

(2022) J Biomol Struct Dyn 40: 8324-8331

PubMed: 33870857 Search on PubMed
DOI: https://doi.org/10.1080/07391102.2021.1911852
Primary Citation of Related Structures:
6ZIJ, 6ZIP

PubMed Abstract:
Multi-copper oxidases are capable of coupling the one-electron oxidation of four substrate equivalents to the four-electron reduction of dioxygen to two molecules of water. This process takes place at the trinuclear copper center of the enzymes. Previously, the main catalytic stages for three-domain (3D) laccases have been identified. However, for bacterial small two-domain (2D) laccases several questions remain to be answered. One of them is the nature of the protonation events upon the reductive cleavage of dioxygen to water. In 3D laccases, acidic residues play a key role in the protonation mechanisms. In this study, the role of the Arg240 residue, located within the T2 tunnel of 2D laccase from Streptomyces griseoflavus Ac-993, was investigated. X-ray structural analysis and kinetic characterization of two mutants, R240A and R240H, have provided support for a role of this residue in the protonation events. Communicated by Ramaswamy H. Sarma.

Organizational Affiliation

Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia.

Macromolecule Content

Total Structure Weight: 210.77 kDa
Atom Count: 14,022
Modelled Residue Count: 1,663
Deposited Residue Count: 1,932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two-domain laccase	A, B, C, D, E A, B, C, D, E, F	322	Streptomyces griseoflavus	Mutation(s): 1 EC: 1.10.3.2
UniProt
Find proteins for A0A0M4FJ81 (Streptomyces griseoflavus) Explore A0A0M4FJ81 Go to UniProtKB: A0A0M4FJ81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M4FJ81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain TA [auth F] SDF format, chain Z [auth C] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain TA [auth F] MOL2 format, chain Z [auth C]	I [auth A], KA [auth E], LA [auth E], TA [auth F], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain TA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain I [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain TA [auth F] Focus chain Z [auth C]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] G [auth A] BA [auth D], CA [auth D], DA [auth D], EA [auth D], G [auth A], H [auth A], HA [auth E], IA [auth E], JA [auth E], K [auth A], L [auth A], MA [auth E], NA [auth E], P [auth B], Q [auth B], QA [auth F], RA [auth F], S [auth B], SA [auth F], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B]	J [auth A], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]
OXY (Subject of Investigation/LOI) Query on OXY Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain T [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain T [auth B]	FA [auth D] M [auth A] N [auth A] OA [auth E] PA [auth E] FA [auth D], M [auth A], N [auth A], OA [auth E], PA [auth E], T [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain T [auth B] Interactions & Density Focus chain FA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain T [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain O [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain O [auth A]	AA [auth C], GA [auth D], O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain O [auth A] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain O [auth A]