6I3L | pdb_00006i3l

Bilirubin oxidase from Myrothecium verrucaria, mutant W396F

PDB DOI: https://doi.org/10.2210/pdb6I3L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Albifimbria verrucaria
Expression System: Aspergillus oryzae
Mutation(s): Yes

Deposited: 2018-11-06 Released: 2019-10-02
Deposition Author(s): Koval, T., Svecova, L., Skalova, T., Kolenko, P., Duskova, J., Ostergaard, L.H., Dohnalek, J.
Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund, Czech Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.196 (Depositor), 0.146 (DCC)
R-Value Work:
0.159 (Depositor)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.

Koval, T., Svecova, L., Ostergaard, L.H., Skalova, T., Duskova, J., Hasek, J., Kolenko, P., Fejfarova, K., Stransky, J., Trundova, M., Dohnalek, J.

(2019) Sci Rep 9: 13700-13700

PubMed: 31548583 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-019-50105-3
Primary Citation Related Structures:
6I3J, 6I3K, 6I3L

PubMed Abstract:
Unlike any protein studied so far, the active site of bilirubin oxidase from Myrothecium verrucaria contains a unique type of covalent link between tryptophan and histidine side chains. The role of this post-translational modification in substrate binding and oxidation is not sufficiently understood. Our structural and mutational studies provide evidence that this Trp396-His398 adduct modifies T1 copper coordination and is an important part of the substrate binding and oxidation site. The presence of the adduct is crucial for oxidation of substituted phenols and it substantially influences the rate of oxidation of bilirubin. Additionally, we bring the first structure of bilirubin oxidase in complex with one of its products, ferricyanide ion, interacting with the modified tryptophan side chain, Arg356 and the active site-forming loop 393-398. The results imply that structurally and chemically distinct types of substrates, including bilirubin, utilize the Trp-His adduct mainly for binding and to a smaller extent for electron transfer.

Organizational Affiliation

Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Průmyslová 595, 252 50, Vestec, Czech Republic. tomas.koval@ibt.cas.cz.

Macromolecule Content

Total Structure Weight: 123.86 kDa
Atom Count: 10,164
Modeled Residue Count: 1,068
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bilirubin oxidase	A, B	534	Albifimbria verrucaria	Mutation(s): 1 EC: 1.3.3.5
UniProt
Find proteins for Q12737 (Albifimbria verrucaria) Explore Q12737 Go to UniProtKB: Q12737
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12737
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	3		N-Glycosylation	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	K [auth A], L [auth A], W [auth B], X [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain W [auth B] Focus chain X [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain Q [auth A] SDF format, chain Z [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain CA [auth B] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] M [auth A] N [auth A] AA [auth B], BA [auth B], CA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain Z [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] S [auth B] G [auth A], H [auth A], I [auth A], J [auth A], S [auth B], T [auth B], U [auth B], V [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 S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain DA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain DA [auth B]	DA [auth B], R [auth A]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain R [auth A] Interactions & Density Focus chain DA [auth B] Focus chain R [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.196 (Depositor), 0.146 (DCC)
R-Value Work: 0.159 (Depositor)
R-Value Observed: 0.161 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.25	α = 90
b = 200.663	β = 90
c = 217.121	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-10-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2015043
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/15_003/0000447
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/16_013/0001776
European Regional Development Fund	Czech Republic	CZ.1.05/1.1.00/02.0109
Czech Academy of Sciences	Czech Republic	86652036

Revision History (Full details and data files)

Version 1.0: 2019-10-02
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-05-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary