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PDBsum entry 1dff
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the escherichia coli peptide deformylase.
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Authors
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M.K.Chan,
W.Gong,
P.T.Rajagopalan,
B.Hao,
C.M.Tsai,
D.Pei.
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Ref.
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Biochemistry, 1997,
36,
13904-13909.
[DOI no: ]
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PubMed id
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Abstract
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Protein synthesis in bacteria involves the formylation and deformylation of the
N-terminal methionine. As eukaryotic organisms differ in their protein
biosynthetic mechanisms, peptide deformylase, the bacterial enzyme responsible
for deformylation, represents a potential target for antibiotic studies. Here we
report the crystallization and 2.9 A X-ray structure solution of the zinc
containing Escherichia coli peptide deformylase. While the primary sequence,
tertiary structure, and use of coordinated cysteine suggest that E. coli
deformylase belongs to a new subfamily of metalloproteases, the environment
around the metal appears to have strong geometric similarity to the active sites
of the thermolysin family. This suggests a possible similarity in their
hydrolytic mechanisms. Another important issue is the origin of the enzyme's
specificity for N-formylated over N-acetylated substrates. Based on the
structure, the specificity appears to result from hydrogen-bonding interactions
which orient the substrate for cleavage, and steric factors which physically
limit the size of the N-terminal carbonyl group.
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