6I3J

Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 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

  • DOI: https://doi.org/10.1038/s41598-019-50105-3
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bilirubin oxidase
A, B
534Albifimbria verrucariaMutation(s): 0 
EC: 1.3.3.5
UniProt
Find proteins for Q12737 (Albifimbria verrucaria)
Explore Q12737 
Go to UniProtKB:  Q12737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12737
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FC6 (Subject of Investigation/LOI)
Query on FC6

Download Ideal Coordinates CCD File 
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
SIN
Query on SIN

Download Ideal Coordinates CCD File 
GA [auth B],
HA [auth B],
O [auth A],
P [auth A],
Q [auth A]
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
PGR
Query on PGR

Download Ideal Coordinates CCD File 
LA [auth B]R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
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
CL
Query on CL

Download Ideal Coordinates CCD File 
W [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.382α = 90
b = 203.846β = 90
c = 226.744γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015043
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/15_003/0000447
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/16_013/0001776
European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0109
Czech Academy of SciencesCzech Republic86652036

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