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PDBsum entry 1e5s
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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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Structure of proline 3-Hydroxylase. Evolution of the family of 2-Oxoglutarate dependent oxygenases.
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Authors
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I.J.Clifton,
L.C.Hsueh,
J.E.Baldwin,
K.Harlos,
C.J.Schofield.
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Ref.
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Eur J Biochem, 2001,
268,
6625-6636.
[DOI no: ]
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PubMed id
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Abstract
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Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative
reactions in a range of metabolic processes including the hydroxylation of
proline and lysine residues during the post-translational modification of
collagen. 2-OG oxygenases commonly require ascorbate for full activity. In the
vitamin C deficient disease, scurvy, reduced activity of 2-OG oxygenases results
in impaired formation of collagen. Here we report the crystal structure of
bacterial proline 3-hydroxylase from Streptomyces sp., an enzyme which
hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing
oxidation of a free alpha-amino acid. Structures were obtained for the enzyme in
the absence of iron (to 2.3A resolution, R=20.2%, Rfree=25.3%) and that
complexed to iron (II) (to 2.4A resolution, R=19.8%, Rfree=22.6%). The structure
contains conserved motifs present in other 2-OG oxygenases including a 'jelly
roll' beta strand core and residues binding iron and 2-oxoglutarate, consistent
with divergent evolution within the extended family. The structure differs
significantly from many other 2-OG oxygenases in possessing a discrete
C-terminal helical domain. Analysis of the structure suggests a model for
proline binding and a mechanism for uncoupling of proline and 2-OG turnover.
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Figure 1.
Fig. 1 Reaction summary. Reactions catalysed by
mononuclear nonhaem iron oxygenases (A) proline 3-hydroxylase
(P-3-H) (B) proline-4-hydroxylase (C) one of the reactions
catalysed by deacetoxycephalosporin C synthase (DAOCS) (D)
isopenicillin N synthase (IPNS) (E) clavaminic acid synthase
(CAS) (F) p-hydroxyphenylpyruvate dioxygenase (HPPD).
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Figure 4.
Fig. 4 View of the P-3-H active site. The active site of
the enzyme (molecule A) cocrystallized with iron(II) sulfate.
The  -barrel core
is in green, the iron binding ligands in purple, the iron in
orange and the N-terminal region and C-terminal domain in
magenta. The ferrous iron is ligated by the side chains of
His107, Asp109 and His158. Note: (a) Arg168, Ser170 and His135
which are probably involved in binding 2-OG; (b) Arg95, Arg97,
Arg122 and His43 which may bind the proline carboxylate; (c) the
disordered loop (in orange) containing six sequential acidic
residues, which may bind the imino group of proline.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
Eur J Biochem
(2001,
268,
6625-6636)
copyright 2001.
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