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* Residue conservation analysis
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Enzyme class:
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Chain E:
E.C.3.4.21.62
- subtilisin.
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Reaction:
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Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.
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Eur J Biochem
166:673-692
(1987)
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PubMed id:
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The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry.
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W.Bode,
E.Papamokos,
D.Musil.
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ABSTRACT
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Triclinic crystals of the complex formed by eglin with subtilisin Carlsberg were
analyzed by X-ray diffraction. The crystal and molecular structure of this
complex was determined with data that extended to 0.12-nm resolution by a
combination of Patterson search methods and isomorphous replacement techniques.
Its structure was refined to a crystallographic R value of 0.178 (1.0-0.12 nm)
using an energy-restraint least-squares procedure. The complete subtilisin
molecule could be traced without ambiguity in the refined electron density. The
eglin component, from which an amino-terminal segment is cleaved off, is only
defined from Lys8I (i.e. the lysine residue 8 of the inhibitor) onwards. Per
unit cell, 436 fixed solvent molecules and 2 calcium ions were located. In spite
of 84 amino acid replacements and one deletion, subtilisin Carlsberg exhibits a
very similar polypeptide fold to subtilisin BPN'. The root-mean-square
deviations of all alpha-carbon atoms (excluding those at the deletion site) from
models of subtilisin BPN' [Alden, R. A., Birktoft, J. J., Kraut, J., Robertus,
J. D. & Wright, C. S. (1971) Biochem. Biophys. Res. Commun. 45, 337-344] and
subtilisin Novo [Drenth, J., Hol, W. G. J., Jansonius, J. N. & Kockoek, R.
(1972) Eur. J. Biochem. 25, 177-181] are 0.077 nm and 0.103 nm. Most of these
deviations result from global shifts rather than changes of the local geometry.
The single-residue deletion at position 56 affects only the surrounding
conformation. Two sites of high electron density and close distances to
surrounding oxygen ligands have been found in the Carlsberg enzyme which are
probably occupied by calcium ions. Eglin consists of a twisted four-stranded
beta-sheet flanked by an alpha-helix and by an exposed proteinase binding loop
on opposite sides. Around the reactive site, Leu45I-Asp46I, this loop is mainly
stabilized by electrostatic/hydrogen bond interactions with the side chains of
two arginine residues which project from the hydrophobic core [Bode, W.,
Papamokos, E., Musil, D., Seemüller, W. & Fritz, H. (1986) EMBO J. 5,
813-818]. The reactive site loop conformation resembles that found in other
'small' proteinase inhibitors. The scissile peptide bond is not cleaved but its
carbonyl group is slightly distorted from planar geometry. Most of the
intermolecular contacts are contributed by the nine residues of the
reactive-site loop Gly40I-Arg48I.(ABSTRACT TRUNCATED AT 400 WORDS)
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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PDB codes:
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PDB code:
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PDB code:
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J Biol Chem,
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PDB code:
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J.S.Fetrow,
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Appl Environ Microbiol,
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The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species.
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FEBS J,
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PDB code:
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Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.
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PDB code:
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Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity.
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PDB codes:
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I.Botos,
E.E.Melnikov,
S.Cherry,
J.E.Tropea,
A.G.Khalatova,
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The crystal structure of the proprotein processing proteinase furin explains its stringent specificity.
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P.Fuentes-Prior,
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PDB codes:
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M.T.Record,
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Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
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PDB code:
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L.Yu,
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Biol Chem,
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Stopped flow fluorescence energy transfer measurement of the rate constants describing the reversible formation and the irreversible rearrangement of the elastase-alpha1-proteinase inhibitor complex.
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|
| |
Proc Natl Acad Sci U S A,
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PDB code:
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J.R.Martin,
F.A.Mulder,
Y.Karimi-Nejad,
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The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site.
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| |
Structure,
5,
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PDB code:
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A.K.Saxena,
T.P.Singh,
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| |
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PDB code:
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L.Zhang,
and
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Hydrophilicity of cavities in proteins.
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M.L.Remerowski,
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