6I3J | pdb_00006i3j

Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide

PDB DOI: https://doi.org/10.2210/pdb6I3J/pdb

Classification: OXIDOREDUCTASE
Organism(s): Albifimbria verrucaria
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2018-11-06 Released: 2019-10-02
Deposition Author(s): Svecova, L., Koval, T., 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: 2.59 Å
R-Value Free:
0.226 (Depositor), 0.190 (DCC)
R-Value Work:
0.160 (Depositor), 0.168 (DCC)
R-Value Observed:
0.162 (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: 125.99 kDa
Atom Count: 9,511
Modeled Residue Count: 1,067
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): 0 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

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 3
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	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FC6 (Subject of Investigation/LOI) Query on FC6 Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] FA [auth B] BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], K [auth A], L [auth A], M [auth A], N [auth A]	HEXACYANOFERRATE(3-) C₆ Fe N₆ HCMVSLMENOCDCK-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	GA [auth B], HA [auth B], O [auth A], P [auth A], Q [auth A]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
PGR Query on PGR Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] MOL2 format, chain LA [auth B] mmCIF format, chain LA [auth B]	LA [auth B]	R-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-GSVOUGTGSA-N		Interactions Focus chain LA [auth B] Interactions & Density Focus chain LA [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] 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 X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [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 X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [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 X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] G [auth A] H [auth A] I [auth A] J [auth A] AA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], X [auth B], Y [auth B], Z [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A] mmCIF format, chain W [auth A]	W [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A]	IA [auth B] JA [auth B] KA [auth B] R [auth A] S [auth A] IA [auth B], JA [auth B], KA [auth B], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.226 (Depositor), 0.190 (DCC)
R-Value Work: 0.160 (Depositor), 0.168 (DCC)
R-Value Observed: 0.162 (Depositor)

Diffraction Data:

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.382	α = 90
b = 203.846	β = 90
c = 226.744	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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 1.1: 2019-10-30
Changes: Advisory, Data collection, Derived calculations
Version 1.2: 2020-04-22
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary