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PDBsum entry 4mlv
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References listed in PDB file
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Key reference
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Title
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Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the bacillus megaterium enzyme at near-Atomic resolution.
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Authors
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N.Azim,
E.Deery,
M.J.Warren,
B.A.Wolfenden,
P.Erskine,
J.B.Cooper,
A.Coker,
S.P.Wood,
M.Akhtar.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2014,
70,
744-751.
[DOI no: ]
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PubMed id
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Abstract
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The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC
2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in
which four molecules of the monopyrrole porphobilinogen are condensed to form a
linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is
covalently linked by a thioether bridge to an invariant cysteine residue (Cys241
in the Bacillus megaterium enzyme). The cofactor is extended during the reaction
by the sequential addition of the four substrate molecules, which are released
as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged
form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from
this species at high resolution, showing that the cofactor becomes progressively
oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved
PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which
both pyrrole rings are approximately coplanar. In contrast, the oxidized
cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form,
in which the C atom at the bridging α-position of the outer pyrrole ring is
very clearly in a tetrahedral configuration. It is suggested that the pink
colour of the freshly purified protein is owing to the presence of the
dipyrromethene form of the cofactor which, in the structure reported here,
adopts the same conformation as the fully reduced dipyrromethane form.
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