3KW7

Crystal structure of LacB from Trametes sp. AH28-2

PDB DOI: https://doi.org/10.2210/pdb3KW7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trametes sp. AH28-2
Mutation(s): No

Deposited: 2009-12-01 Released: 2010-03-09
Deposition Author(s): Ge, H.H., Teng, M.K., Niu, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.44 Å
R-Value Free: 0.292
R-Value Work: 0.223
R-Value Observed: 0.226

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structure of native laccase B from Trametes sp. AH28-2

Ge, H.H., Gao, Y.X., Hong, Y.Z., Zhang, M., Xiao, Y.Z., Teng, M.K., Niu, L.W.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 254-258

PubMed: 20208154 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309110000084
Primary Citation of Related Structures:
3KW7

PubMed Abstract:
Fungal laccases are oxidoreductases that belong to the multinuclear copper-containing oxidases. They are able to oxidize a wide range of substrates, preferably phenolic compounds, which makes them suitable for employment in the bioremediation of soil and water as well as in other biotechnological applications. Here, the structural analysis of natural laccase B (LacB) from Trametes sp. AH28-2 is presented. This structure provides the opportunity to study the natural post-translational modifications of the enzyme. The overall fold shows a high homology to those of previously analyzed laccases with known three-dimensional structure. However, LacB contains a new structural element, a protruding loop near the substrate-binding site, compared with the previously reported laccase structures. This unique structural feature may be involved in modulation of the substrate recognition of LacB.

Organizational Affiliation

Modern Experiment Technology Center and School of Life Sciences, Anhui University, Hefei 230039, People's Republic of China.

Macromolecule Content

Total Structure Weight: 110.89 kDa
Atom Count: 7,825
Modelled Residue Count: 1,004
Deposited Residue Count: 1,004
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laccase B	A, B	502	Trametes sp. AH28-2	Mutation(s): 0 EC: 1.10.3.2
UniProt
Find proteins for Q5I7J0 (Trametes sp. AH28-2) Explore Q5I7J0 Go to UniProtKB: Q5I7J0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7J0
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	K [auth A], L [auth A], Q [auth B], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] M [auth B] G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-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 M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.44 Å
R-Value Free: 0.292
R-Value Work: 0.223
R-Value Observed: 0.226
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.778	α = 90
b = 98.778	β = 90
c = 149.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Ge, H.H.

Teng, M.K.

Niu, L.W.

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-25
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-09
Changes: Structure summary