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PDBsum entry 1ppe
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protein Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
1ppe

 

 

 

 

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Contents
Protein chains
223 a.a. *
29 a.a. *
Waters ×140
* Residue conservation analysis
PDB id:
1ppe
Name: Hydrolase/hydrolase inhibitor
Title: The refined 2.0 angstroms x-ray crystal structure of the complex formed between bovine beta-trypsin and cmti-i, a trypsin inhibitor from squash seeds (cucurbita maxima): topological similarity of the squash seed inhibitors with the carboxypeptidase a inhibitor from potatoes
Structure: Trypsin. Chain: e. Engineered: yes. Trypsin inhibitor cmti-i. Chain: i. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: seed.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.151    
Authors: W.Bode,R.Huber
Key ref: W.Bode et al. (1989). The refined 2.0 A X-ray crystal structure of the complex formed between bovine beta-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes. Febs Lett, 242, 285-292. PubMed id: 2914611
Date:
24-Oct-91     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus
Seq:
Struc: 		246 a.a.
223 a.a.
Protein chain
Pfam   ArchSchema ?
P01074  (ITR1_CUCMA) -  Trypsin inhibitor 1 from Cucurbita maxima
Seq:
Struc: 		29 a.a.
29 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain E: E.C.3.4.21.4  - trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

 

 
Febs Lett 242:285-292 (1989)
PubMed id: 2914611  
 
 
The refined 2.0 A X-ray crystal structure of the complex formed between bovine beta-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes.
W.Bode, H.J.Greyling, R.Huber, J.Otlewski, T.Wilusz.
 
  ABSTRACT  
 
The stoichiometric complex formed between bovine beta-trypsin and the Cucurbita maxima trypsin inhibitor I (CMTI-I) was crystallized and its X-ray crystal structure determined using Patterson search techniques. Its structure has been crystallographically refined to a final R value of 0.152 (6.0-2.0 A). CMTI-I is of ellipsoidal shape; it lacks helices or beta-sheets, but consists of turns and connecting short polypeptide stretches. The disulfide pairing is CYS-3I-20I, Cys-10I-22I and Cys-16I-28I. According to the polypeptide fold and disulfide connectivity its structure resembles that of the carboxypeptidase A inhibitor from potatoes. Thirteen of the 29 inhibitor residues are in direct contact with trypsin; most of them are in the primary binding segment Val-2I (P4)-Glu-9I (P4') which contains the reactive site bond Arg-5I-Ile-6I and is in a conformation observed also for other serine proteinase inhibitors.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19077275 A.Heitz, O.Avrutina, D.Le-Nguyen, U.Diederichsen, J.F.Hernandez, J.Gracy, H.Kolmar, and L.Chiche (2008).
Knottin cyclization: Impact on Structure and Dynamics.
  BMC Struct Biol, 8, 54.  
16899489 A.D.van Dijk, and A.M.Bonvin (2006).
Solvated docking: introducing water into the modelling of biomolecular complexes.
  Bioinformatics, 22, 2340-2347.  
16636277 E.S.Radisky, J.M.Lee, C.J.Lu, and D.E.Koshland (2006).
Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates.
  Proc Natl Acad Sci U S A, 103, 6835-6840.
PDB codes: 2age 2agg 2agi 2ah4
  17142906 M.Azarkan, A.Garcia-Pino, R.Dibiani, L.Wyns, R.Loris, and D.Baeyens-Volant (2006).
Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1239-1242.  
16556998 P.Atiwetin, S.Harada, and K.Kamei (2006).
Serine proteinase inhibitor from wax gourd (Benincasa hispida [Thunb] Cogn.) seeds.
  Biosci Biotechnol Biochem, 70, 743-745.  
16544327 Y.J.Liu, C.S.Cheng, S.M.Lai, M.P.Hsu, C.S.Chen, and P.C.Lyu (2006).
Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids.
  Proteins, 63, 777-786.
PDB code: 1ti5
15775973 J.Otlewski, F.Jelen, M.Zakrzewska, and A.Oleksy (2005).
The many faces of protease-protein inhibitor interaction.
  EMBO J, 24, 1303-1310.  
16336125 O.Avrutina, H.U.Schmoldt, D.Gabrijelcic-Geiger, D.Le Nguyen, C.P.Sommerhoff, U.Diederichsen, and H.Kolmar (2005).
Trypsin inhibition by macrocyclic and open-chain variants of the squash inhibitor MCoTI-II.
  Biol Chem, 386, 1301-1306.  
14681383 J.C.Gelly, J.Gracy, Q.Kaas, D.Le-Nguyen, A.Heitz, and L.Chiche (2004).
The KNOTTIN website and database: a new information system dedicated to the knottin scaffold.
  Nucleic Acids Res, 32, D156-D159.  
12554935 J.Aÿ, K.Hilpert, N.Krauss, J.Schneider-Mergener, and W.Höhne (2003).
Structure of a hybrid squash inhibitor in complex with porcine pancreatic elastase at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 247-254.
PDB code: 1mcv
12482862 N.L.Daly, R.J.Clark, and D.J.Craik (2003).
Disulfide folding pathways of cystine knot proteins. Tying the knot within the circular backbone of the cyclotides.
  J Biol Chem, 278, 6314-6322.
PDB code: 1n1u
12112698 F.R.Melo, D.J.Rigden, O.L.Franco, L.V.Mello, M.B.Ary, M.F.Grossi de Sá, and C.Bloch (2002).
Inhibition of trypsin by cowpea thionin: characterization, molecular modeling, and docking.
  Proteins, 48, 311-319.  
11856298 O.L.Franco, D.J.Rigden, F.R.Melo, and M.F.Grossi-De-Sá (2002).
Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases.
  Eur J Biochem, 269, 397-412.  
12198301 R.Thaimattam, E.Tykarska, A.Bierzynski, G.M.Sheldrick, and M.Jaskolski (2002).
Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination.
  Acta Crystallogr D Biol Crystallogr, 58, 1448-1461.
PDB code: 1lu0
  10716179 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.
  Protein Sci, 9, 273-279.
PDB codes: 1bxj 2v1v 2v2y
11004551 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.
  Biochim Biophys Acta, 1480, 6.  
10404643 B.Huang, T.B.Ng, W.P.Fong, C.C.Wan, and H.W.Yeung (1999).
Isolation of a trypsin inhibitor with deletion of N-terminal pentapeptide from the seeds of Momordica cochinchinensis, the Chinese drug mubiezhi.
  Int J Biochem Cell Biol, 31, 707-715.  
10102985 H.Czapinska, and J.Otlewski (1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
  Eur J Biochem, 260, 571-595.  
10508777 P.J.Pereira, V.Lozanov, A.Patthy, R.Huber, W.Bode, S.Pongor, and S.Strobl (1999).
Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution.
  Structure, 7, 1079-1088.
PDB code: 1clv
10089404 R.Helland, G.I.Berglund, J.Otlewski, W.Apostoluk, O.A.Andersen, N.P.Willassen, and A.O.Smalås (1999).
High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes.
  Acta Crystallogr D Biol Crystallogr, 55, 139-148.
PDB codes: 2btc 2sta 2stb
10400675 S.Lu, P.Deng, X.Liu, J.Luo, R.Han, X.Gu, S.Liang, X.Wang, F.Li, V.Lozanov, A.Patthy, and S.Pongor (1999).
Solution structure of the major alpha-amylase inhibitor of the crop plant amaranth.
  J Biol Chem, 274, 20473-20478.
PDB code: 1qfd
9799488 C.A.Behnke, V.C.Yee, I.L.Trong, L.C.Pedersen, R.E.Stenkamp, S.S.Kim, G.R.Reeck, and D.C.Teller (1998).
Structural determinants of the bifunctional corn Hageman factor inhibitor: x-ray crystal structure at 1.95 A resolution.
  Biochemistry, 37, 15277-15288.
PDB codes: 1bea 1bfa
  9514268 J.Liu, Y.Gong, O.Prakash, L.Wen, I.Lee, J.K.Huang, and R.Krishnamoorthi (1998).
NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI)-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family.
  Protein Sci, 7, 132-141.  
9675278 J.Polanowska, I.Krokoszynska, H.Czapinska, W.Watorek, M.Dadlez, and J.Otlewski (1998).
Specificity of human cathepsin G.
  Biochim Biophys Acta, 1386, 189-198.  
9304857 M.Kooman-Gersmann, R.Vogelsang, E.C.Hoogendijk, and P.J.De Wit (1997).
Assignment of amino acid residues of the AVR9 peptide of Cladosporium fulvum that determine elicitor activity.
  Mol Plant Microbe Interact, 10, 821-829.  
9032072 P.R.Mittl, S.Di Marco, G.Fendrich, G.Pohlig, J.Heim, C.Sommerhoff, H.Fritz, J.P.Priestle, and M.G.Grütter (1997).
A new structural class of serine protease inhibitors revealed by the structure of the hirustasin-kallikrein complex.
  Structure, 5, 253-264.
PDB code: 1hia
9311976 R.Lapatto, U.Krengel, H.A.Schreuder, A.Arkema, B.de Boer, K.H.Kalk, W.G.Hol, P.D.Grootenhuis, J.W.Mulders, R.Dijkema, H.J.Theunissen, and B.W.Dijkstra (1997).
X-ray structure of antistasin at 1.9 A resolution and its modelled complex with blood coagulation factor Xa.
  EMBO J, 16, 5151-5161.
PDB code: 1skz
8718849 E.S.Stavridi, K.O'Malley, C.M.Lukacs, W.T.Moore, J.D.Lambris, D.W.Christianson, H.Rubin, and B.S.Cooperman (1996).
Structural change in alpha-chymotrypsin induced by complexation with alpha 1-antichymotrypsin as seen by enhanced sensitivity to proteolysis.
  Biochemistry, 35, 10608-10615.  
8634282 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.
  Biochemistry, 35, 1516-1524.
PDB code: 1mit
8823186 J.Liu, O.Prakash, Y.Huang, L.Wen, J.J.Wen, J.K.Huang, and R.Krishnamoorthi (1996).
Internal mobility of reactive-site-hydrolyzed recombinant Cucurbita maxima trypsin inhibitor-V characterized by NMR spectroscopy: evidence for differential stabilization of newly formed C- and N-termini.
  Biochemistry, 35, 12503-12510.  
8952509 M.Price-Carter, W.R.Gray, and D.P.Goldenberg (1996).
Folding of omega-conotoxins. 2. Influence of precursor sequences and protein disulfide isomerase.
  Biochemistry, 35, 15547-15557.  
8954162 R.H.Voss, U.Ermler, L.O.Essen, G.Wenzl, Y.M.Kim, and P.Flecker (1996).
Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28-nm resolution. Structural peculiarities in a folded protein conformation.
  Eur J Biochem, 242, 122-131.
PDB code: 1k9b
7552703 S.L.Lin, and R.Nussinov (1995).
A disulphide-reinforced structural scaffold shared by small proteins with diverse functions.
  Nat Struct Biol, 2, 835-837.  
  8060538 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.
  Biol Chem Hoppe Seyler, 375, 289-291.  
7922044 K.Huang, N.C.Strynadka, V.D.Bernard, R.J.Peanasky, and M.N.James (1994).
The molecular structure of the complex of Ascaris chymotrypsin/elastase inhibitor with porcine elastase.
  Structure, 2, 679-689.
PDB code: 1eai
  8003965 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).
  Protein Sci, 3, 291-302.
PDB code: 2let
  7849598 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.
  Protein Sci, 3, 1833-1839.  
8210313 A.T.Brünger, and M.Nilges (1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
  Q Rev Biophys, 26, 49.  
  8443596 D.Le-Nguyen, A.Heitz, L.Chiche, M.el Hajji, and B.Castro (1993).
Characterization and 2D NMR study of the stable [9-21, 15-27] 2 disulfide intermediate in the folding of the 3 disulfide trypsin inhibitor EETI II.
  Protein Sci, 2, 165-174.  
1544459 A.V.Efimov (1992).
A novel super-secondary structure of beta-proteins. A triple-strand corner.
  FEBS Lett, 298, 261-265.  
1409678 C.B.Breton, T.Blisnick, H.Jouin, J.C.Barale, T.Rabilloud, G.Langsley, and L.H.Pereira da Silva (1992).
Plasmodium chabaudi p68 serine protease activity required for merozoite entry into mouse erythrocytes.
  Proc Natl Acad Sci U S A, 89, 9647-9651.  
  1304349 W.Bode, D.Turk, and A.Karshikov (1992).
The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.
  Protein Sci, 1, 426-471.
PDB codes: 1ai8 1aix
1541261 W.Bode, and R.Huber (1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
  Eur J Biochem, 204, 433-451.  
2085383 O.Matsumoto, T.Taga, T.Higashi, M.Matsushima, and K.Machida (1990).
Complex formation by bovine trypsin and a tetrapeptide (Leu-Arg-Pro-Gly-NH2): X-ray structure analysis of the complex in the orthorhombic crystal form with low molecular packing density.
  J Protein Chem, 9, 589-593.  
2226434 W.Bode, D.Turk, and J.Stürzebecher (1990).
Geometry of binding of the benzamidine- and arginine-based inhibitors N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-pipe ridine (NAPAP) and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) to human alpha-thrombin. X-ray crystallographic determination of the NAPAP-trypsin complex and modeling of NAPAP-thrombin and MQPA-thrombin.
  Eur J Biochem, 193, 175-182.
PDB code: 1ppc
2678630 T.E.Creighton, and N.J.Darby (1989).
Functional evolutionary divergence of proteolytic enzymes and their inhibitors.
  Trends Biochem Sci, 14, 319-324.  
  2583108 W.Bode, I.Mayr, U.Baumann, R.Huber, S.R.Stone, and J.Hofsteenge (1989).
The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.
  EMBO J, 8, 3467-3475.
PDB code: 1ppb
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 codes are shown on the right.

 

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