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PDBsum entry 1ke2
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Hydrolase/hydrolase inhibitor
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PDB id
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1ke2
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Contents |
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* Residue conservation analysis
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Obsolete entry |
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PDB id:
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| Name: |
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Hydrolase/hydrolase inhibitor
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Title:
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Pseudomonas serine-carboxyl proteinase complexed with the inhibitor chymostatin (this enzyme renamed "sedolisin" in 2003)
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Structure:
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Serine-carboxyl proteinase. Chain: a. Synonym: pscp, pseudomonapepsin, pepstatin-insensitive carboxyl proteinase. Engineered: yes. Chymostatin. Chain: b. Engineered: yes
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Source:
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Pseudomonas sp.. Organism_taxid: 306. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Streptomyces lavendulae, mc524-c1. Organism_taxid: 1914. Other_details: the inhibitor was chemically synthesized.
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Biol. unit:
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Tetramer (from
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Resolution:
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2.00Å
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R-factor:
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0.187
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R-free:
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0.243
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Authors:
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A.Wlodawer,M.Li,A.Gustchina,Z.Dauter,K.Uchida,H.Oyama,N.E.Goldfarb, B.M.Dunn,K.Oda
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Key ref:
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A.Wlodawer
et al.
(2001).
Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase.
Biochemistry,
40,
15602-15611.
PubMed id:
DOI:
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Date:
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14-Nov-01
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Release date:
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12-Dec-01
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PROCHECK
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Headers
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References
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P42790
(PICP_PSESR) -
Pseudomonalisin from Pseudomonas sp. (strain 101)
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Seq:
Struc:
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587 a.a.
367 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Biochemistry
40:15602-15611
(2001)
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PubMed id:
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Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase.
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A.Wlodawer,
M.Li,
A.Gustchina,
Z.Dauter,
K.Uchida,
H.Oyama,
N.E.Goldfarb,
B.M.Dunn,
K.Oda.
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ABSTRACT
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Crystal structures of the serine-carboxyl proteinase from Pseudomonas sp. 101
(PSCP), complexed with a number of inhibitors, have been solved and refined at
high- to atomic-level resolution. All of these inhibitors (tyrostatin,
pseudo-tyrostatin, AcIPF, AcIAF, and chymostatin, as well as previously studied
iodotyrostatin and pseudo-iodotyrostatin) make covalent bonds to the active site
Ser287 through their aldehyde moieties, while their side chains occupy subsites
S1-S4 of the enzyme. The mode of binding of the inhibitors is almost identical
for their P1 and P2 side chains, while significant differences are observed for
P3 and P4 (if present). Kinetic parameters for the binding of these nanomolar
inhibitors to PSCP have been established and correlated with the observed mode
of binding. The preferences of this enzyme for a larger side chain in P2 as well
as Tyr or Phe in P1 are explained by the size, shape, and characteristics of the
S2 and S1 regions of the protein structure, respectively. Networks of hydrogen
bonds involving glutamic and aspartic acids have been analyzed for the
atomic-resolution structure of the native enzyme. PSCP contains a
calcium-binding site that consists of Asp328, Asp348, three amide carbonyl
groups, and a water molecule, in almost perfect octahedral coordination. The
presence of Ca(2+) cation is necessary for the activity of the enzyme.
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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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J.Guhaniyogi,
I.Sohar,
K.Das,
A.M.Stock,
and
P.Lobel
(2009).
Crystal structure and autoactivation pathway of the precursor form of human tripeptidyl-peptidase 1, the enzyme deficient in late infantile ceroid lipofuscinosis.
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J Biol Chem,
284,
3985-3997.
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PDB code:
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W.Nishii,
K.Kubota,
and
K.Takahashi
(2009).
The P1 and P1' residue specificities of physarolisin I, a serine-carboxyl peptidase from the true slime mold Physarum polycephalum.
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Biosci Biotechnol Biochem,
73,
1168-1171.
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A.Langkilde,
S.M.Kristensen,
L.Lo Leggio,
A.Mølgaard,
J.H.Jensen,
A.R.Houk,
J.C.Navarro Poulsen,
S.Kauppinen,
and
S.Larsen
(2008).
Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase.
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Acta Crystallogr D Biol Crystallogr,
64,
851-863.
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PDB code:
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O.D.Ekici,
M.Paetzel,
and
R.E.Dalbey
(2008).
Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration.
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Protein Sci,
17,
2023-2037.
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Q.Xu,
H.B.Guo,
A.Wlodawer,
T.Nakayama,
and
H.Guo
(2007).
The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As.
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Biochemistry,
46,
3784-3792.
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A.Okubo,
M.Li,
M.Ashida,
H.Oyama,
A.Gustchina,
K.Oda,
B.M.Dunn,
A.Wlodawer,
and
T.Nakayama
(2006).
Processing, catalytic activity and crystal structures of kumamolisin-As with an engineered active site.
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FEBS J,
273,
2563-2576.
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PDB codes:
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N.Watanabe,
T.Akiba,
R.Kanai,
and
K.Harata
(2006).
Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.
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Acta Crystallogr D Biol Crystallogr,
62,
784-792.
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PDB codes:
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A.Korostelev,
M.O.Fenley,
and
M.S.Chapman
(2004).
Impact of a Poisson-Boltzmann electrostatic restraint on protein structures refined at medium resolution.
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Acta Crystallogr D Biol Crystallogr,
60,
1786-1794.
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A.Wlodawer,
M.Li,
A.Gustchina,
N.Tsuruoka,
M.Ashida,
H.Minakata,
H.Oyama,
K.Oda,
T.Nishino,
and
T.Nakayama
(2004).
Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity.
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J Biol Chem,
279,
21500-21510.
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PDB codes:
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J.Brynda,
P.Rezácová,
M.Fábry,
M.Horejsí,
R.Stouracová,
M.Soucek,
M.Hradílek,
J.Konvalinka,
and
J.Sedlácek
(2004).
Inhibitor binding at the protein interface in crystals of a HIV-1 protease complex.
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Acta Crystallogr D Biol Crystallogr,
60,
1943-1948.
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PDB code:
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A.Wlodawer,
S.R.Durell,
M.Li,
H.Oyama,
K.Oda,
and
B.M.Dunn
(2003).
A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases.
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BMC Struct Biol,
3,
8.
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PDB code:
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M.Comellas-Bigler,
P.Fuentes-Prior,
K.Maskos,
R.Huber,
H.Oyama,
K.Uchida,
B.M.Dunn,
K.Oda,
and
W.Bode
(2002).
The 1.4 a crystal structure of kumamolysin: a thermostable serine-carboxyl-type proteinase.
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Structure,
10,
865-876.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
