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PDBsum entry 1cti
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Proteinase inhibitor (trypsin)
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PDB id
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1cti
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J Mol Biol
210:635-648
(1989)
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PubMed id:
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Determination of the complete three-dimensional structure of the trypsin inhibitor from squash seeds in aqueous solution by nuclear magnetic resonance and a combination of distance geometry and dynamical simulated annealing.
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T.A.Holak,
D.Gondol,
J.Otlewski,
T.Wilusz.
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ABSTRACT
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The complete three-dimensional structure of the trypsin inhibitor from seeds of
the squash Cucurbita maxima in aqueous solution was determined on the basis of
324 interproton distance constraints, 80 non-nuclear Overhauser effect
distances, and 22 hydrogen-bonding constraints, supplemented by 27 phi backbone
angle constraints derived from nuclear magnetic resonance measurements. The
nuclear magnetic resonance input data were converted to the distance constraints
in a semiquantitative manner after a sequence specific assignment of 1H spectra
was obtained using two-dimensional nuclear magnetic resonance techniques.
Stereospecific assignments were obtained for 17 of the 48 prochiral centers of
the squash trypsin inhibitor using the floating chirality assignment introduced
at the dynamical simulated annealing stage of the calculations. A total of 34
structures calculated by a hybrid distance geometry-dynamical simulated
annealing method exhibit well-defined positions for both backbone and side-chain
atoms. The average atomic root-mean-square difference between the individual
structures and the minimized mean structure is 0.35(+/- 0.08) A for the backbone
atoms and 0.89(+/- 0.17) A for all heavy atoms. The precision of the structure
determination is discussed and correlated to the experimental input data.
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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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P.Atiwetin,
S.Harada,
and
K.Kamei
(2006).
Serine proteinase inhibitor from wax gourd (Benincasa hispida [Thunb] Cogn.) seeds.
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Biosci Biotechnol Biochem,
70,
743-745.
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J.L.Arolas,
L.D'Silva,
G.M.Popowicz,
F.X.Aviles,
T.A.Holak,
and
S.Ventura
(2005).
NMR structural characterization and computational predictions of the major intermediate in oxidative folding of leech carboxypeptidase inhibitor.
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Structure,
13,
1193-1202.
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PDB codes:
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G.Dubin,
M.Krajewski,
G.Popowicz,
J.Stec-Niemczyk,
M.Bochtler,
J.Potempa,
A.Dubin,
and
T.A.Holak
(2003).
A novel class of cysteine protease inhibitors: solution structure of staphostatin A from Staphylococcus aureus.
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Biochemistry,
42,
13449-13456.
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PDB code:
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L.Jouvensal,
L.Quillien,
E.Ferrasson,
Y.Rahbé,
J.Guéguen,
and
F.Vovelle
(2003).
PA1b, an insecticidal protein extracted from pea seeds (Pisum sativum): 1H-2-D NMR study and molecular modeling.
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Biochemistry,
42,
11915-11923.
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PDB code:
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R.Thaimattam,
E.Tykarska,
A.Bierzynski,
G.M.Sheldrick,
and
M.Jaskolski
(2002).
Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination.
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Acta Crystallogr D Biol Crystallogr,
58,
1448-1461.
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PDB code:
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R.Stoll,
C.Renner,
M.Zweckstetter,
M.Brüggert,
D.Ambrosius,
S.Palme,
R.A.Engh,
M.Golob,
I.Breibach,
R.Buettner,
W.Voelter,
T.A.Holak,
and
A.K.Bosserhoff
(2001).
The extracellular human melanoma inhibitory activity (MIA) protein adopts an SH3 domain-like fold.
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EMBO J,
20,
340-349.
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PDB code:
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H.Zheng
(2000).
Electronic structure of trypsin inhibitor from squash seeds in aqueous solution.
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Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics,
62,
5500-5508.
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I.Zhukov,
L.Jaroszewski,
and
A.Bierzyński
(2000).
Conservative mutation Met8 --> Leu affects the folding process and structural stability of squash trypsin inhibitor CMTI-I.
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Protein Sci,
9,
273-279.
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PDB codes:
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K.Kamei,
S.Sato,
N.Hamato,
R.Takano,
K.Ohshima,
R.Yamamoto,
T.Nishino,
H.Kato,
and
S.Hara
(2000).
Effect of P(2)' site tryptophan and P(20)' site deletion of Momordica charantia trypsin inhibitor II on inhibition of proteinases.
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Biochim Biophys Acta,
1480,
6.
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T.Cierpicki,
J.Bania,
and
J.Otlewski
(2000).
NMR solution structure of Apis mellifera chymotrypsin/cathepsin G inhibitor-1 (AMCI-1): structural similarity with Ascaris protease inhibitors.
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Protein Sci,
9,
976-984.
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PDB code:
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T.Weber,
R.Baumgartner,
C.Renner,
M.A.Marahiel,
and
T.A.Holak
(2000).
Solution structure of PCP, a prototype for the peptidyl carrier domains of modular peptide synthetases.
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Structure,
8,
407-418.
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PDB code:
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J.Badger,
R.A.Kumar,
P.Yip,
and
S.Szalma
(1999).
New features and enhancements in the X-PLOR computer program.
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Proteins,
35,
25-33.
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J.P.Tam,
Y.A.Lu,
J.L.Yang,
and
K.W.Chiu
(1999).
An unusual structural motif of antimicrobial peptides containing end-to-end macrocycle and cystine-knot disulfides.
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Proc Natl Acad Sci U S A,
96,
8913-8918.
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S.Gourinath,
A.Srinivasan,
and
T.P.Singh
(1999).
Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.9 A resolution.
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Acta Crystallogr D Biol Crystallogr,
55,
25-30.
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PDB code:
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H.J.Schirra,
C.Renner,
M.Czisch,
M.Huber-Wunderlich,
T.A.Holak,
and
R.Glockshuber
(1998).
Structure of reduced DsbA from Escherichia coli in solution.
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Biochemistry,
37,
6263-6276.
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PDB codes:
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J.P.Tam,
and
Y.A.Lu
(1998).
A biomimetic strategy in the synthesis and fragmentation of cyclic protein.
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Protein Sci,
7,
1583-1592.
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J.Polanowska,
I.Krokoszynska,
H.Czapinska,
W.Watorek,
M.Dadlez,
and
J.Otlewski
(1998).
Specificity of human cathepsin G.
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Biochim Biophys Acta,
1386,
189-198.
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P.Mühlhahn,
M.Zweckstetter,
J.Georgescu,
C.Ciosto,
C.Renner,
M.Lanzendörfer,
K.Lang,
D.Ambrosius,
M.Baier,
R.Kurth,
and
T.A.Holak
(1998).
Structure of interleukin 16 resembles a PDZ domain with an occluded peptide binding site.
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Nat Struct Biol,
5,
682-686.
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PDB code:
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W.Kalus,
M.Zweckstetter,
C.Renner,
Y.Sanchez,
J.Georgescu,
M.Grol,
D.Demuth,
R.Schumacher,
C.Dony,
K.Lang,
and
T.A.Holak
(1998).
Structure of the IGF-binding domain of the insulin-like growth factor-binding protein-5 (IGFBP-5): implications for IGF and IGF-I receptor interactions.
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EMBO J,
17,
6558-6572.
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PDB code:
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P.Fucini,
C.Renner,
C.Herberhold,
A.A.Noegel,
and
T.A.Holak
(1997).
The repeating segments of the F-actin cross-linking gelation factor (ABP-120) have an immunoglobulin-like fold.
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Nat Struct Biol,
4,
223-230.
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PDB code:
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R.Stoll,
W.Voelter,
and
T.A.Holak
(1997).
Conformation of thymosin beta 9 in water/fluoroalcohol solution determined by NMR spectroscopy.
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Biopolymers,
41,
623-634.
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PDB code:
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E.Kohfeldt,
W.Göhring,
U.Mayer,
M.Zweckstetter,
T.A.Holak,
M.L.Chu,
and
R.Timpl
(1996).
Conversion of the Kunitz-type module of collagen VI into a highly active trypsin inhibitor by site-directed mutagenesis.
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Eur J Biochem,
238,
333-340.
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J.Liu,
O.Prakash,
M.Cai,
Y.Gong,
Y.Huang,
L.Wen,
J.J.Wen,
J.K.Huang,
and
R.Krishnamoorthi
(1996).
Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.
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Biochemistry,
35,
1516-1524.
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PDB code:
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M.Price-Carter,
W.R.Gray,
and
D.P.Goldenberg
(1996).
Folding of omega-conotoxins. 2. Influence of precursor sequences and protein disulfide isomerase.
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Biochemistry,
35,
15547-15557.
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M.Zweckstetter,
M.Czisch,
U.Mayer,
M.L.Chu,
W.Zinth,
R.Timpl,
and
T.A.Holak
(1996).
Structure and multiple conformations of the kunitz-type domain from human type VI collagen alpha3(VI) chain in solution.
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Structure,
4,
195-209.
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B.L.Grasberger,
G.M.Clore,
and
A.M.Gronenborn
(1994).
High-resolution structure of Ascaris trypsin inhibitor in solution: direct evidence for a pH-induced conformational transition in the reactive site.
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Structure,
2,
669-678.
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PDB codes:
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J.Rózycki,
G.Kupryszewski,
K.Rolka,
U.Ragnarsson,
T.Zbyryt,
I.Krokoszyńska,
and
T.Wilusz
(1994).
New active analogues of Cucurbita maxima trypsin inhibitor III (CMTI-III) modified in the non-contact region.
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Biol Chem Hoppe Seyler,
375,
21-23.
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J.Rózycki,
G.Kupryszewski,
K.Rolka,
U.Ragnarsson,
T.Zbyryt,
I.Krokoszyńska,
and
T.Wilusz
(1994).
Analogues of Cucurbita maxima trypsin inhibitor III (CMTI-III) with elastase inhibitory activity.
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Biol Chem Hoppe Seyler,
375,
289-291.
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K.J.Nielsen,
D.Alewood,
J.Andrews,
S.B.Kent,
and
D.J.Craik
(1994).
An 1H NMR determination of the three-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor from Ecballium elaterium (EETI-II).
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Protein Sci,
3,
291-302.
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PDB code:
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P.K.Pallaghy,
K.J.Nielsen,
D.J.Craik,
and
R.S.Norton
(1994).
A common structural motif incorporating a cystine knot and a triple-stranded beta-sheet in toxic and inhibitory polypeptides.
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Protein Sci,
3,
1833-1839.
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A.M.Bonvin,
J.A.Rullmann,
R.M.Lamerichs,
R.Boelens,
and
R.Kaptein
(1993).
"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
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Proteins,
15,
385-400.
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PDB code:
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A.T.Brünger,
and
M.Nilges
(1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
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Q Rev Biophys,
26,
49.
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D.F.Mierke,
and
H.Kessler
(1993).
Improved molecular dynamics simulations for the determination of peptide structures.
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Biopolymers,
33,
1003-1017.
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J.J.Skalicky,
W.J.Metzler,
D.J.Ciesla,
A.Galdes,
and
A.Pardi
(1993).
Solution structure of the calcium channel antagonist omega-conotoxin GVIA.
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Protein Sci,
2,
1591-1603.
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M.Czisch,
M.Schleicher,
S.Hörger,
W.Voelter,
and
T.A.Holak
(1993).
Conformation of thymosin beta 4 in water determined by NMR spectroscopy.
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Eur J Biochem,
218,
335-344.
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M.J.Sutcliffe
(1993).
Representing an ensemble of NMR-derived protein structures by a single structure.
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Protein Sci,
2,
936-944.
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M.W.MacArthur,
and
J.M.Thornton
(1993).
Conformational analysis of protein structures derived from NMR data.
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Proteins,
17,
232-251.
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M.J.Sippl,
M.Hendlich,
and
P.Lackner
(1992).
Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4.
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Protein Sci,
1,
625-640.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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
codes are
shown on the right.
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Links
