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PDBsum entry 1q0c
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Oxidoreductase
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PDB id
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1q0c
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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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Crystallographic comparison of manganese- And iron-Dependent homoprotocatechuate 2,3-Dioxygenases.
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Authors
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M.W.Vetting,
L.P.Wackett,
L.Que,
J.D.Lipscomb,
D.H.Ohlendorf.
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Ref.
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J Bacteriol, 2004,
186,
1945-1958.
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PubMed id
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Abstract
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The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated
from Arthrobacter globiformis and Brevibacterium fuscum have been determined to
high resolution. These enzymes exhibit 83% sequence identity, yet their
activities depend on different transition metals, Mn2+ and Fe2+, respectively.
The structures allow the origins of metal ion selectivity and aspects of the
molecular mechanism to be examined in detail. The homotetrameric enzymes belong
to the type I family of extradiol dioxygenases (vicinal oxygen chelate
superfamily); each monomer has four betaalphabetabetabeta modules forming two
structurally homologous N-terminal and C-terminal barrel-shaped domains. The
active-site metal is located in the C-terminal barrel and is ligated by two
equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to
three water molecules. The first and second coordination spheres of these
enzymes are virtually identical (root mean square difference over all atoms,
0.19 A), suggesting that the metal selectivity must be due to changes at a
significant distance from the metal and/or changes that occur during folding.
The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal
asymmetrically at sites trans to the two imidazole ligands and interacts with a
unique, mobile C-terminal loop. The loop closes over the bound substrate,
presumably to seal the active site as the oxygen activation process commences.
An "open" coordination site trans to E267 is the likely binding site for O2. The
geometry of the enzyme-substrate complexes suggests that if a transiently formed
metal-superoxide complex attacks the substrate without dissociation from the
metal, it must do so at the C-3 position. Second-sphere active-site residues
that are positioned to interact with the HPCA and/or bound O2 during catalysis
are identified and discussed in the context of current mechanistic hypotheses.
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