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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41598-019-50105-3
  • Primary Citation of Related Structures:  

  • 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 bi ...

    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

    Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark.,Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Průmyslová 595, 252 50, Vestec, Czech Republic.,Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Průmyslová 595, 252 50, Vestec, Czech Republic. jan.dohnalek@ibt.cas.cz.,Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19, Praha 1, Czech Republic.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bilirubin oxidase
A, B
534Albifimbria verrucariaMutation(s): 0 
EC: 1.3.3.5
Find proteins for Q12737 (Albifimbria verrucaria)
Go to UniProtKB:  Q12737
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FC6
Query on FC6

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A, B
HEXACYANOFERRATE(3-)
FERRI(III)HEXACYANIDE
C6 Fe N6
HCMVSLMENOCDCK-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SIN
Query on SIN

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A, B
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
PGR
Query on PGR

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B
R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
 Ligand Interaction
BMA
Query on BMA

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A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
CU
Query on CU

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A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.160 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 134.382α = 90.00
b = 203.846β = 90.00
c = 226.744γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-30
    Type: Advisory, Data collection, Derived calculations