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PDBsum entry 2b6n
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References listed in PDB file
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Key reference
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Title
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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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Authors
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R.Helland,
A.N.Larsen,
A.O.Smalås,
N.P.Willassen.
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Ref.
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FEBS J, 2006,
273,
61-71.
[DOI no: ]
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PubMed id
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Abstract
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Proteins from organisms living in extreme conditions are of particular interest
because of their potential for being templates for redesign of enzymes both in
biotechnological and other industries. The crystal structure of a proteinase
K-like enzyme from a psychrotroph Serratia species has been solved to 1.8 A. The
structure has been compared with the structures of proteinase K from
Tritirachium album Limber and Vibrio sp. PA44 in order to reveal structural
explanations for differences in biophysical properties. The Serratia peptidase
shares around 40 and 64% identity with the Tritirachium and Vibrio peptidases,
respectively. The fold of the three enzymes is essentially identical, with minor
exceptions in surface loops. One calcium binding site is found in the Serratia
peptidase, in contrast to the Tritirachium and Vibrio peptidases which have two
and three, respectively. A disulfide bridge close to the S2 site in the Serratia
and Vibrio peptidases, an extensive hydrogen bond network in a tight loop close
to the substrate binding site in the Serratia peptidase and different amino acid
sequences in the S4 sites are expected to cause different substrate specificity
in the three enzymes. The more negative surface potential of the Serratia
peptidase, along with a disulfide bridge close to the S2 binding site of a
substrate, is also expected to contribute to the overall lower binding affinity
observed for the Serratia peptidase. Clear electron density for a tripeptide,
probably a proteolysis product, was found in the S' sites of the substrate
binding cleft.
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Figure 1.
Fig. 1. Structural alignment of SPRK, PRK and VPRK.
Helices (red tubes) and sheets (yellow arrows) are according to
SPRK. Residues belonging to the S1 site are shaded blue and
residues belonging to the S4 site are shaded light blue.
*represents residues that are involved both in the S1 and S4
sites. Residues forming the calcium binding site found in SPRK
(and VPRK) are shaded green, residues forming the ‘strong’
calcium binding site in PRK (and in VPRK) are shaded khaki, and
residues forming the calcium sites unique for either PRK or VPRK
are shaded pale green.
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Figure 5.
Fig. 5. Stereo plot illustrating the tight loop forming
the S2 binding site. Red is SPRK, green is PRK and blue is VPRK.
Labels and distances in the loop refer to SPRK. The stabilizing
hydrogen bonding network formed by residues Asn97, Ser99 and
Ser101 in SPRK is displayed as ball-and-stick models. A similar
network is not as strong in PRK and VPRK due to a shorter Ser97
in VPRK and a too-long Asn99 in PRK. The loop is anchored to the
rest of the molecule in SPRK and VPRK by a disulfide bridge
between Cys98 and Cys66 (Asp98 in PRK). The catalytic His69 is
displayed as ball-and-stick model in order to illustrate the
orientation of the loop relative to the binding site.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS J
(2006,
273,
61-71)
copyright 2006.
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