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PDBsum entry 2f91
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Hydrolase/hydrolase inhibitor
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PDB id
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2f91
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References listed in PDB file
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Key reference
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Title
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Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis.
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Authors
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K.Fodor,
V.Harmat,
R.Neutze,
L.Szilágyi,
L.Gráf,
G.Katona.
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Ref.
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Biochemistry, 2006,
45,
2114-2121.
[DOI no: ]
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PubMed id
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Abstract
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Atomic resolution (<or=1.2 A) serine protease intermediate structures
revealed that the strength of the hydrogen bonds between the enzyme and the
substrate changed during catalysis. The well-conserved hydrogen bonds of
antiparallel beta-sheet between the enzyme and the substrate become
significantly shorter in the transition from a Michaelis complex analogue
(Pontastacus leptodactylus (narrow-fingered crayfish) trypsin (CFT) in complex
with Schistocerca gregaria (desert locust) trypsin inhibitor (SGTI) at 1.2 A
resolution) to an acyl-enzyme intermediate (N-acetyl-Asn-Pro-Ile acyl-enzyme
intermediate of porcine pancreatic elastase at 0.95 A resolution) presumably
synchronously with the nucleophilic attack on the carbonyl carbon atom of the
scissile peptide bond. This is interpreted as an active mechanism that utilizes
the energy released from the stronger hydrogen bonds to overcome the energetic
barrier of the nucleophilic attack by the hydroxyl group of the catalytic
serine. In the CFT:SGTI complex this hydrogen bond shortening may be hindered by
the 27I-32I disulfide bridge and Asn-15I of SGTI. The position of the catalytic
histidine changes slightly as it adapts to the different nucleophilic attacker
during the transition from the Michaelis complex to the acyl-enzyme state, and
simultaneously its interaction with Asp-102 and Ser-214 becomes stronger. The
oxyanion hole hydrogen bonds provide additional stabilization for acyl-ester
bond in the acyl-enzyme than for scissile peptide bond of the Michaelis complex.
Significant deviation from planarity is not observed in the reactive bonds of
either the Michaelis complex or the acyl-enzyme. In the Michaelis complex the
electron distribution of the carbonyl bond is distorted toward the oxygen atom
compared to other peptide bonds in the structure, which indicates the
polarization effect of the oxyanion hole.
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Secondary reference #1
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Title
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Extended intermolecular interactions in a serine protease-Canonical inhibitor complex account for strong and highly specific inhibition.
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Authors
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K.Fodor,
V.Harmat,
C.Hetényi,
J.Kardos,
J.Antal,
A.Perczel,
A.Patthy,
G.Katona,
L.Gráf.
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Ref.
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J Mol Biol, 2005,
350,
156-169.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Extended binding region determining taxon
specificity of SGTI. The crystal structure of the crayfish
trypsin (magenta)-SGTI (light blue) complex superimposed over
the representative model (MD, 180 ps step) of bovine trypsin
(dark blue)-SGTI (green) complex. Conserved structural motives
of trypsin are shown in grey. N, O and S atoms are shown in
atomic colors. Hydrogen bonds are shown as green shaded lines.
Black and red labels are used for the enzymes and inhibitors,
respectively. (a) Stereo view of the P1' residue accommodated in
the S1' site. Distances between the charged groups of the
enzymes and the P1' lysine amino group are 7.67 Å, 8.22
Å and 6.19 Å for E35 and D60b of crayfish trypsin
and K60 of bovine trypsin, respectively. The conformation of the
side-chain of the P1' lysine is stabilized by an intramolecular
hydrogen bond. (b) Binding of the P[4]'-P[5]' region (stereo
view) is dominated by hydrophobic contacts. (c) Binding of the
P[12]-P[6] region by the crayfish enzyme is realized by several
hydrogen bonds. (d) Binding of the P[12]-P[6] region by the
bovine enzyme. The hydrogen bonds of the P[8] threonine are
lost, while stacking interaction is established between the P[9]
proline and Pro173. The Figure was generated by MOLSCRIPT.52
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Figure 6.
Figure 6. Shape adaptation upon binding of arthropod
trypsin inhibitor SGTI to the surface of crayfish trypsin. (a)
The structural alignment of the free (rose) and bound (light
blue) forms of SGTI reveals three regions of major backbone
conformation difference: the N-terminal segment (not shown),
residues 20-26 (P[10]-P[4]) and residue 31 (P[2]'). The latter
two are parts of the binding region (O and N atoms shown in
atomic colors). Carbon atoms of residues in the P[7]-P[4] and
P[2]' regions are colored orange and dark blue for the free and
bound form of SGTI, respectively. (b) Cartoon of SGTI binding to
the enzyme. SGTI is shown in light blue (segments of the binding
region with different backbone conformations in the free and
bound form) and black (remaining parts). Cysteine and P[1]
arginine side-chains of SGTI are shown, while some of its
sub-sites are labeled in red. The enzyme surface is shown in
magenta with black labels for the substrate binding sub-sites.
Upper panel: conformation of the free form is preformed to
recognize the S[12]-S[8] and S[4]'-S[5]' sub-sites of the enzyme
(shown as broken green arrows). In regions P[10]-P[4] and P[2]'
conformation changes should occur, causing the rotation of the
P[3]-P[1]' and P[4]'-P[5]' as well (light blue arrows). Lower
panel: these conformational changes facilitate the build-up of
an extended interaction network between SGTI and the enzyme
(green arrows) in the complex.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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