5ZLM | pdb_00005zlm

Mutation in the trinuclear site of CotA-laccase: H491C mutant, PH 8.0

PDB DOI: https://doi.org/10.2210/pdb5ZLM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-03-28 Released: 2018-05-16
Deposition Author(s): Xie, T., Liu, Z.C., Wang, G.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.182 (Depositor), 0.199 (DCC)
R-Value Work:
0.161 (Depositor)
R-Value Observed:
0.162 (Depositor)

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

Structural Insight into the Allosteric Coupling of Cu1 Site and Trinuclear Cu Cluster in CotA Laccase.

Xie, T., Liu, Z., Wang, G.

(2018) Chembiochem 19: 1502-1506

PubMed: 29722464 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201800236
Primary Citation Related Structures:
5ZLJ, 5ZLK, 5ZLL, 5ZLM

PubMed Abstract:
In laccase, type 1 copper (Cu1) was connected to the trinuclear copper center (TNC) by the conserved Cys-His bridge. An allosteric coupling between the two redox sites has been reported; however, the molecular mechanism underlining the allosteric coupling is unknown. In this study, ligands of the two type 3 copper sites, including His491 and His493, in CotA were mutated to Cys or Ala. The crystal structures revealed that mutations at His491 and His493 caused rearrangement of the hydrogen-bond network and geometric distortion of the TNC, which severely impaired the activities of mutants H493A, H493C, and H491C. In addition, the change in TNC affected hydrogen bonds around Cys492 in the mutants and led to Cu1 being partially reduced. These results not only decipher the mechanism of allosteric coupling between Cu1 and TNC in laccase, but also pave the way for laccase protein engineering.

Organizational Affiliation

Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P.R. China.

Macromolecule Content

Total Structure Weight: 59.47 kDa
Atom Count: 4,798
Modeled Residue Count: 502
Deposited Residue Count: 513
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spore coat protein A	A	513	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 1 Gene Names: cotA, pig, BSU06300 EC: 1.10.3.2 (UniProt), 1.3.3.5 (UniProt)
UniProt
Find proteins for P07788 (Bacillus subtilis (strain 168)) Explore P07788 Go to UniProtKB: P07788
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.182 (Depositor), 0.199 (DCC)
R-Value Work: 0.161 (Depositor)
R-Value Observed: 0.162 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.709	α = 90
b = 101.709	β = 90
c = 135.769	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Xie, T.

Liu, Z.C.

Wang, G.G.

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2020-01-29
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary