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PDBsum entry 3mat
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Hydrolase/hydrolase inhibitor
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PDB id
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3mat
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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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Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, Mutant, And inhibited enzymes for the mechanism of catalysis.
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Authors
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W.T.Lowther,
A.M.Orville,
D.T.Madden,
S.Lim,
D.H.Rich,
B.W.Matthews.
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Ref.
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Biochemistry, 1999,
38,
7678-7688.
[DOI no: ]
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PubMed id
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Abstract
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By improving the expression and purification of Escherichia coli methionine
aminopeptidase (eMetAP) and using slightly different crystallization conditions,
the resolution of the parent structure was extended from 2.4 to 1.9 A
resolution. This has permitted visualization of the coordination geometry and
solvent structure of the active-site dinuclear metal center. One solvent
molecule (likely a mu-hydroxide) bridges the trigonal bipyramidal (Co1) and
octahedral (Co2) cobalt ions. A second solvent (possibly a hydroxide ion) is
bound terminally to Co2. A monovalent cation binding site was also identified
about 13 A away from the metal center at an interface between the two subdomains
of the protein. The first structure of a substrate-like inhibitor,
(3R)-amino-(2S)-hydroxyheptanoyl-L-Ala-L-Leu-L-Val-L-Phe-OMe, bound to a
methionine aminopeptidase, has also been determined. This inhibitor coordinates
the metal center through four interactions as follows: (i) ligation of the
N-terminal (3R)-nitrogen to Co2, (ii, iii) bridging coordination of the
(2S)-hydroxyl group, and (iv) terminal ligation to Co1 by the keto oxygen of the
pseudo-peptide linkage. Inhibitor binding occurs with the displacement of two
solvent ligands and the expansion of the coordination sphere of Co1. In addition
to the tetradentate, bis-chelate metal coordination, the substrate analogue
forms hydrogen bonds with His79 and His178, two conserved residues within the
active site of all MetAPs. To evaluate their importance in catalysis His79 and
His178 were replaced with alanine. Both substitutions, but especially that of
His79, reduce activity. The structure of the His79Ala apoenzyme and the
comparison of its electronic absorption spectra with other variants suggest that
the loss in activity is not due to a conformational change or a defective metal
center. Two different reaction mechanisms are proposed and are compared to those
of related enzymes. These results also suggest that inhibitors analogous to that
reported here may be useful in preventing angiogenesis in cancer and in the
treatment of microbial and fungal infections.
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Secondary reference #1
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Title
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The anti-Angiogenic agent fumagillin covalently modifies a conserved active-Site histidine in the escherichia coli methionine aminopeptidase.
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Authors
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W.T.Lowther,
D.A.Mcmillen,
A.M.Orville,
B.W.Matthews.
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Ref.
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Proc Natl Acad Sci U S A, 1998,
95,
12153-12157.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. The anti-angiogenesis compounds fumagillin,
ovalicin, and TNP-470. The intact epoxide attached to C3 is
required for anti-angiogenic activity. Numbering scheme taken
from Griffith et al. (14).
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Figure 5.
Fig. 5. Hypothetical model of ovalicin bound covalently
to His-79 in the active site of E. coli MetAP. (A) An
energy-minimized model of the complex was made assuming sp3
atoms at C2 and C3 after formation of the covalent bond between
C2 and N  2 of
His-79. The His-79-ovalicin complex was rotated about the His-79
C^  -C^
 and C^
-C^  bonds
until the C6 keto oxygen atom of ovalicin was within
approximately 2.5 Å of each Co(II) ion. As illustrated via
a space filling model (B), access to the metal center is almost
completely occluded. Color scheme: protein carbon atoms (gray),
ovalicin carbon atoms (green), nitrogen (blue), oxygen (red),
cobalt (cyan), and sulfur (yellow). Energy minimizations were
performed by using the DISCOVER program in the InsightII package
(Biosym Technologies, San Diego/Molecular Simulations, Waltham,
MA). The figure was made by using MIDASPLUS (University of
California, San Francisco Computer Graphics Laboratory).
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Secondary reference #2
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Title
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Structure of the cobalt-Dependent methionine aminopeptidase from escherichia coli: a new type of proteolytic enzyme.
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Authors
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S.L.Roderick,
B.W.Matthews.
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Ref.
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Biochemistry, 1993,
32,
3907-3912.
[DOI no: ]
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PubMed id
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