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PDBsum entry 1esb
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References listed in PDB file
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Key reference
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Title
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Direct structural observation of an acyl-Enzyme intermediate in the hydrolysis of an ester substrate by elastase.
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Authors
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X.Ding,
B.F.Rasmussen,
G.A.Petsko,
D.Ringe.
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Ref.
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Biochemistry, 1994,
33,
9285-9293.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
95%.
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Abstract
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The method of X-ray crystallographic cryoenzymology has been used to determine
the crystal structure of a kinetically significant species on the reaction
pathway of a crystalline enzyme. The structure of a specific acyl-enzyme
intermediate in the elastase-catalyzed hydrolysis of the
N-carbobenzoxy-L-alanine p-nitrophenyl ester has been determined and refined
against X-ray diffraction data at 2.3-A resolution. The difference Fourier
electron density map clearly shows electron density for the trapped acyl-enzyme.
The acyl-enzyme was formed at -26 degrees C and was stabilized at -55 degrees C
during data collection, taking advantage of the glass transition in protein
dynamics that occurs at around -50 degrees C.
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Secondary reference #1
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Title
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Crystal structure of the covalent complex formed by a peptidyl alpha,Alpha-Difluoro-Beta-Keto amide with porcine pancreatic elastase at 1.78 angstroms resolution
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Authors
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L.H.Takahashi,
R.Radhakrishnan,
R.E.Rosenfield junior,
E.F.Meyer junior,
D.A.Trainor.
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Ref.
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j am chem soc, 1989,
111,
3368.
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Secondary reference #2
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Title
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Structure of native porcine pancreatic elastase at 1.65 a resolutions.
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Authors
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E.Meyer,
G.Cole,
R.Radhakrishnan,
O.Epp.
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Ref.
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Acta Crystallogr B, 1988,
44,
26-38.
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PubMed id
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Secondary reference #3
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Title
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Structures of product and inhibitor complexes of streptomyces griseus protease a at 1.8 a resolution. A model for serine protease catalysis.
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Authors
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M.N.James,
A.R.Sielecki,
G.D.Brayer,
L.T.Delbaere,
C.A.Bauer.
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Ref.
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J Mol Biol, 1980,
144,
43-88.
[DOI no: ]
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PubMed id
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Figure 3.
FIG:. 3. Difference electron density maps computed with coefficients IE',\ - IP,I. phases hC in the region
ofthe active ite of SGPA. These are fragment maps in which a portin of the molecule was not included in.~
the structure factor calculation.
(a) AcPro-Ala-Pro-Phe-OH, peptide 1, the atoms excluded from the phase calculation were 0' of
Ser195 and th terminal carboxyl oxygen atom of the tetrapeptide product which binds in the oxyanion
bindin site. The 2 largest positive peaks correspond to these expected atomic position. The 3rd peak
just below that for OY of Ser195 corresponds to a water molecule not included in the phasng.
(b) The corresponding atomic model ofthe tetrapeptide aldehyde (onl P, Pro and P, Phe shown) with
the electron ensity for Oy Her195 and the two water moleules 0366 and 0361 which were not mcluded in
the calculation.
In both (a) and (b) the electron density cotour surfaces are kO.23 eA3 and the negative density is
represented by broken lines. This and subsequent Figures have been made with the aid of the MMS-X
interactive graphics (Barry et al., 1976).
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Figure 9.
FIG. 9. Comparison ofthe binding modes ofthe Ac-Pro-Ala-Pro-Phe-OH product (solid, thin lines) and
the aldehyde inhibitor (broken lines). The enzyme conformation is that obseved in complex I. The P, Pro
ring hs a changed coformation in the aldehyde. The carbonyl carbon atom of the aldehyde is I.73 A
distant from Oy of Ser195.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #4
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Title
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Formation of stable crystalline enzyme-Substrate intermediates at sub-Zero temperatures.
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Authors
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A.L.Fink,
A.I.Ahmed.
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Ref.
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Nature, 1976,
263,
294-297.
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PubMed id
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Secondary reference #5
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Title
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Crystal structure of elastase-Substrate complex at -- 55 degrees c.
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Authors
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T.Alber,
G.A.Petsko,
D.Tsernoglou.
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Ref.
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Nature, 1976,
263,
297-300.
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PubMed id
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