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PDBsum entry 1qpa
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Oxidoreductase
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PDB id
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1qpa
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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The crystal structure of lignin peroxidase at 1.70 a resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle.
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Authors
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T.Choinowski,
W.Blodig,
K.H.Winterhalter,
K.Piontek.
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Ref.
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J Mol Biol, 1999,
286,
809-827.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of lignin peroxidase (LiP) from the white rot fungus
Phanerochaete chrysosporium was refined to an R-factor of 16.2 % utilizing
synchrotron data in the resolution range from 10 to 1.7 A. The final model
comprises all 343 amino acid residues, 370 water molecules, the heme, four
carbohydrates, and two calcium ions. Lignin peroxidase shows the typical
peroxidase fold and the heme has a close environment as found in other
peroxidases. During refinement of the LiP model an unprecedented modification of
an amino acid was recognized. The surface residue tryptophan 171 in LiP is
stereospecifically hydroxylated at the Cbeta atom due to an autocatalytic
process. We propose that during the catalytic cycle of LiP a transient radical
at Trp171 occurs that is different from those previously assumed for this type
of peroxidase. Recently, the existence of a second substrate-binding site
centered at Trp171 has been reported, by us which is different from the
"classical heme edge" site found in other peroxidases. Here, we report evidence
for a radical formation at Trp171 using spin trapping, which supports the
concept of Trp171 being a redox active amino acid and being involved in the
oxidation of veratryl alcohol. On the basis of our current model, an electron
pathway from Trp171 to the heme is envisaged, relevant for the oxidation of
veratryl alcohol and possibly lignin. Beside the opening leading to the heme
edge, which can accommodate small aromatic substrate molecules, a smaller
channel giving access to the distal heme pocket was identified that is large
enough for molecules such as hydrogen peroxide. Furthermore, it was found that
in LiP the bond between the heme iron and the Nepsilon2 atom of the proximal
histidine residue is significantly longer than in cytochrome c peroxidase (CcP).
The weaker Fe-N bond in LiP renders the heme more electron deficient and
destabilizes high oxidation states, which could explain the higher redox
potential of LiP as compared to CcP.
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Figure 6.
Figure 6. Stereoscopic view of the (a) proximal and (b)
distal calcium-binding sites in LiP415. Both difference omit
maps are contoured at 15σ. The bonds are shown as broken lines
and the liganding residues and bond lengths are labelled.
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Figure 15.
Figure 15. The molecular surface charge distribution of
LiP415 showing the “back side” of the protein. The negative
potentials on the surface are shaded in red and the positive
potentials in blue. The heme, and several hydrophobic surface
residues at the vicinity of Trp171 are depicted by bonds. The
picture was generated using the program GRASP [Nicholls 1993].
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
286,
809-827)
copyright 1999.
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Secondary reference #1
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Title
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Do carbohydrates play a role in the lignin peroxidase cycle? redox catalysis in the endergonic region of the driving force.
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Authors
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H.E.Schoemaker,
T.K.Lundell,
R.Floris,
T.Glumoff,
K.H.Winterhalter,
K.Piontek.
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Ref.
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Bioorg Med Chem Lett, 1994,
2,
509-519.
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PubMed id
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Secondary reference #2
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Title
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The oxidation of veratryl alcohol, Dimeric lignin models and lignin by lignin peroxidase: the redox cycle revisited
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Authors
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H.E.Schoemaker,
T.K.Lundell,
A.I.Hatakka,
K.Piontek.
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Ref.
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fems microbiol rev, 1994,
13,
321.
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Secondary reference #3
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Title
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Low ph crystal structure of glycosylated lignin peroxidase from phanerochaete chrysosporium at 2.5 a resolution.
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Authors
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K.Piontek,
T.Glumoff,
K.Winterhalter.
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Ref.
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FEBS Lett, 1993,
315,
119-124.
[DOI no: ]
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PubMed id
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