7PUH | pdb_00007puh

Crystal Structure of Two-Domain Laccase mutant H165A/R240H from Streptomyces griseoflavus

PDB DOI: https://doi.org/10.2210/pdb7PUH/pdb

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

Deposited: 2021-09-30 Released: 2022-01-19
Deposition Author(s): Kolyadenko, I., Tishchenko, S., Gabdulkhakov, A.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.157 (Depositor), 0.161 (DCC)
R-Value Work:
0.133 (Depositor), 0.139 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Engineering the Catalytic Properties of Two-Domain Laccase from Streptomyces griseoflavus Ac-993.

Kolyadenko, I., Scherbakova, A., Kovalev, K., Gabdulkhakov, A., Tishchenko, S.

(2021) Int J Mol Sci 23

PubMed: 35008493 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ijms23010065
Primary Citation Related Structures:
7PEN, 7PES, 7PFR, 7PTM, 7PU0, 7PUH

PubMed Abstract:
Laccases catalyze the oxidation of substrates with the concomitant reduction of oxygen to water. Recently, we found that polar residues located in tunnels leading to Cu2 and Cu3 ions control oxygen entrance (His 165) and proton transport (Arg 240) of two-domain laccase (2D) from Streptomyces griseoflavus (SgfSL). In this work, we have focused on optimizing the substrate-binding pocket (SBP) of SgfSL while simultaneously adjusting the oxygen reduction process. SgfSL variants with three single (Met199Ala, Met199Gly, and Tyr230Ala) and three double amino acid residues substitutions (Met199Gly/His165Ala, His165Ala/Arg240His, Met199Gly/Arg240His) were constructed, purified, and investigated. Combination of substitutions in the SBP and in the tunnel leading to Cu2 ion (Met199Gly/Arg240His) increased SgfSL catalytic activity towards ABTS by 5-fold, and towards 2.6-DMP by 16-fold. The high activity of the Met199Gly/Arg240His variant can be explained by the combined effect of the SBP geometry optimization (Met199Gly) and increased proton flux via the tunnel leading to Cu2 ion (Arg240His). Moreover, the variant with Met199Gly and His165Ala mutations did not significantly increase SgfSL's activity, but led to a drastic shift in the optimal pH of 2.6-DMP oxidation. These results indicate that His 165 not only regulates oxygen access, but it also participates in proton transport in 2D laccases.

Organizational Affiliation

Institute of Protein Research RAS, 142290 Pushchino, Russia.

Macromolecule Content

Total Structure Weight: 183.85 kDa
Atom Count: 15,938
Modeled Residue Count: 1,666
Deposited Residue Count: 1,668
Unique protein chains: 1

Macromolecules

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| 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	278	Streptomyces griseoflavus	Mutation(s): 2 EC: 1.10.3.2
UniProt
Find proteins for A0A0M4FJ81 (Streptomyces griseoflavus) Explore A0A0M4FJ81 Go to UniProtKB: A0A0M4FJ81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0M4FJ81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain BA [auth C]	BA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Interactions & Density Focus chain BA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain K [auth A] SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C]	GA [auth D], K [auth A], S [auth B], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain K [auth A] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain K [auth A] Focus chain S [auth B] Focus chain Z [auth C]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File 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 I [auth A] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain RA [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] 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 I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [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] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	CA [auth D] DA [auth D] EA [auth D] G [auth A] H [auth A] CA [auth D], DA [auth D], EA [auth D], G [auth A], H [auth A], HA [auth E], I [auth A], IA [auth E], JA [auth E], KA [auth E], M [auth B], N [auth B], NA [auth F], O [auth B], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], RA [auth F], U [auth C], V [auth C], W [auth C], X [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions 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 I [auth A] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain M [auth B] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density 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 I [auth A] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain M [auth B] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain MA [auth E] SDF format, chain T [auth B] SDF format, chain TA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain MA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain MA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F]	AA [auth C], MA [auth E], T [auth B], TA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain MA [auth E] Focus chain T [auth B] Focus chain TA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain MA [auth E] Focus chain T [auth B] Focus chain TA [auth F]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain LA [auth E] SDF format, chain R [auth B] SDF format, chain SA [auth F] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain Y [auth C]	FA [auth D] J [auth A] LA [auth E] R [auth B] SA [auth F] FA [auth D], J [auth A], LA [auth E], R [auth B], SA [auth F], Y [auth C]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain J [auth A] Focus chain LA [auth E] Focus chain R [auth B] Focus chain SA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain J [auth A] Focus chain LA [auth E] Focus chain R [auth B] Focus chain SA [auth F] Focus chain Y [auth C]