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PDBsum entry 6l1v
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Electron transport
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PDB id
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6l1v
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PDB id:
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| Name: |
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Electron transport
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Title:
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Domain-swapped alcaligenes xylosoxidans azurin dimer
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Structure:
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Azurin-1. Chain: a, c, e, g. Synonym: azn-1,azurin-i. Engineered: yes
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Source:
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Alcaligenes xylosoxydans xylosoxydans. Organism_taxid: 85698. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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2.25Å
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R-factor:
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0.204
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R-free:
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0.230
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Authors:
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R.N.Cahyono,M.Yamanaka,S.Nagao,N.Shibata,Y.Higuchi,S.Hirota
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Key ref:
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R.N.Cahyono
et al.
(2020).
3D domain swapping of azurin from Alcaligenes xylosoxidans.
Metallomics,
12,
337-345.
PubMed id:
DOI:
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Date:
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30-Sep-19
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Release date:
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05-Feb-20
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PROCHECK
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Headers
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References
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P56547
(AZUR1_ALCXX) -
Azurin-1 from Alcaligenes xylosoxydans xylosoxydans
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Seq:
Struc:
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129 a.a.
129 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
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DOI no:
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Metallomics
12:337-345
(2020)
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PubMed id:
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3D domain swapping of azurin from Alcaligenes xylosoxidans.
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R.N.Cahyono,
M.Yamanaka,
S.Nagao,
N.Shibata,
Y.Higuchi,
S.Hirota.
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ABSTRACT
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Protein oligomers have gained interest, owing to their increased knowledge in
cells and promising utilization for future materials. Various proteins have been
shown to 3D domain swap, but there has been no domain swapping report on a blue
copper protein. Here, we found that azurin from Alcaligenes xylosoxidans
oligomerizes by the procedure of 2,2,2-trifluoroethanol addition to Cu(i)-azurin
at pH 5.0, lyophilization, and dissolution at pH 7.0, whereas it slightly
oligomerizes when using Cu(ii)-azurin. The amount of high order oligomers
increased with the addition of Cu(ii) ions to the dissolution process of a
similar procedure for apoazurin, indicating that Cu(ii) ions enhance azurin
oligomerization. The ratio of the absorbance at 460 nm to that at ∼620 nm of
the azurin dimer (Abs460/Abs618 = 0.113) was higher than that of the monomer
(Abs460/Abs622 = 0.067) and the EPR A‖ value of the dimer (5.85 mT) was
slightly smaller than that of the monomer (5.95 mT), indicating a slightly more
rhombic copper coordination for the dimer. The redox potential of the azurin
dimer was 342 ± 5 mV vs. NHE, which was 50 mV higher than that of the monomer.
According to X-ray crystal analysis, the azurin dimer exhibited a domain-swapped
structure, where the N-terminal region containing three β-strands was exchanged
between protomers. The copper coordination structure was tetrahedrally distorted
in the azurin dimer, similar to that in the monomer; however, the Cu-O(Gly45)
bond length was longer for the dimer (monomer, 2.46-2.59 Å; dimer, 2.98-3.25
Å). These results open the door for designing oligomers of blue copper proteins
by domain swapping.
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