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PDBsum entry 5yas
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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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Three-Dimensional structures of enzyme-Substrate complexes of the hydroxynitrile lyase from hevea brasiliensis.
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Authors
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J.Zuegg,
K.Gruber,
M.Gugganig,
U.G.Wagner,
C.Kratky.
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Ref.
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Protein Sci, 1999,
8,
1990-2000.
[DOI no: ]
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PubMed id
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Abstract
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The 3D structures of complexes between the hydroxynitrile lyase from Hevea
brasiliensis (Hb-HNL) and several substrate and/or inhibitor molecules,
including trichloracetaldehyde, hexafluoracetone, acetone, and rhodanide, were
determined by X-ray crystallography. The complex with trichloracetaldehyde
showed a covalent linkage between the protein and the inhibitor, which had
apparently resulted from nucleophilic attack of the catalytic Ser80-Ogamma. All
other complexes showed the substrate or inhibitor molecule merely hydrogen
bonded to the protein. In addition, the native crystal structure of Hb-HNL was
redetermined at cryo-temperature and at room temperature, eliminating previous
uncertainties concerning residual electron density within the active site, and
leading to the observation of two conserved water molecules. One of them was
found to be conserved in all complex structures and appears to have mainly
structural significance. The other water molecule is conserved in all structures
except for the complex with rhodanide; it is hydrogen bonded to the imidazole of
the catalytic His235 and appears to affect the Hb-HNL catalyzed reaction. The
observed 3D structural data suggest implications for the enzyme mechanism. It
appears that the enzyme-catalyzed cyanohydrin formation is unlikely to proceed
via a hemiacetal or hemiketal intermediate covalently attached to the enzyme,
despite the observation of such an intermediate for the complex with
trichloracetaldehyde. Instead, the data are consistent with a mechanism where
the incoming substrate is activated by hydrogen bonding with its carbonyl oxygen
to the Ser80 and Thr11 hydroxy groups. A hydrogen cyanide molecule subsequently
replaces a water molecule and is deprotonated presumably by the His235 base.
Deprotonation is facilitated by the proximity of the positive charge of the
Lys236 side chain.
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Figure 5.
Fig. 5. Residual density within the active site of Hb--HNL for the ~A! F6-acetone, ~B! rhodanide, and ~C! acetone soaks. See caption
to Figure 3 for details.
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The above figure is
reprinted
by permission from the Protein Society:
Protein Sci
(1999,
8,
1990-2000)
copyright 1999.
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Secondary reference #1
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Title
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Hydroxynitrile lyase from hevea brasiliensis: molecular characterization and mechanism of enzyme catalysis.
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Authors
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M.Hasslacher,
C.Kratky,
H.Griengl,
H.Schwab,
S.D.Kohlwein.
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Ref.
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Proteins, 1997,
27,
438-449.
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PubMed id
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Secondary reference #2
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Title
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Crystallization and preliminary X-Ray diffraction studies of a hydroxynitrile lyase from hevea brasiliensis.
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Authors
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U.G.Wagner,
M.Schall,
M.Hasslacher,
M.Hayn,
H.Griengl,
H.Schwab,
C.Kratky.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1996,
52,
591-593.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Diffraction pattem of the 011 plane simulated from the
hkl
file by
the program
ItKLVIEW
of the
CCP4
package (Collaborative
Computational Project, Number 4, 1994).
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #3
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Title
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Mechanism of cyanogenesis: the crystal structure of hydroxynitrile lyase from hevea brasiliensis.
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Authors
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U.G.Wagner,
M.Hasslacher,
H.Griengl,
H.Schwab,
C.Kratky.
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Ref.
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Structure, 1996,
4,
811-822.
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PubMed id
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