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PDBsum entry 1cbw

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protein ligands Protein-protein interface(s) links
Complex (serine protease/inhibitor) PDB id
1cbw
Jmol
Contents
Protein chains
11 a.a.
131 a.a. *
97 a.a. *
58 a.a. *
Ligands
SO4 ×2
Waters ×158
* Residue conservation analysis
PDB id:
1cbw
Name: Complex (serine protease/inhibitor)
Title: Bovine chymotrypsin complexed to bpti
Structure: Bovine chymotrypsin. Chain: a, f. Bovine chymotrypsin. Chain: b, g. Bovine chymotrypsin. Chain: c, h. Bpti. Chain: d, i. Synonym: basic pancreatic trypsin inhibitor
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Biol. unit: Not given
Resolution:
2.60Å     R-factor:   0.192     R-free:   0.251
Authors: T.R.Hynes,A.J.Scheidig,A.A.Kossiakoff
Key ref: A.J.Scheidig et al. (1997). Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities. Protein Sci, 6, 1806-1824. PubMed id: 9300481 DOI: 10.1002/pro.5560060902
Date:
22-Dec-96     Release date:   23-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00767  (CTRB_BOVIN) -  Chymotrypsinogen B
Seq:
Struc:
245 a.a.
11 a.a.
Protein chains
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
Seq:
Struc:
245 a.a.
131 a.a.
Protein chains
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
Seq:
Struc:
245 a.a.
97 a.a.
Protein chains
Pfam   ArchSchema ?
P00974  (BPT1_BOVIN) -  Pancreatic trypsin inhibitor
Seq:
Struc:
100 a.a.
58 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
DOI no: 10.1002/pro.5560060902 Protein Sci 6:1806-1824 (1997)
PubMed id: 9300481  
 
 
Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities.
A.J.Scheidig, T.R.Hynes, L.A.Pelletier, J.A.Wells, A.A.Kossiakoff.
 
  ABSTRACT  
 
The crystal structures of the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) complexed to bovine chymotrypsin (C-APPI) and trypsin (T-APPI) and basic pancreatic trypsin inhibitor (BPTI) bound to chymotrypsin (C-BPTI) have been solved and analyzed at 2.1 A, 1.8 A, and 2.6 A resolution, respectively. APPI and BPTI belong to the Kunitz family of inhibitors, which is characterized by a distinctive tertiary fold with three conserved disulfide bonds. At the specificity-determining site of these inhibitors (P1), residue 15(I)4 is an arginine in APPI and a lysine in BPTI, residue types that are counter to the chymotryptic hydrophobic specificity. In the chymotrypsin complexes, the Arg and Lys P1 side chains of the inhibitors adopt conformations that bend away from the bottom of the binding pocket to interact productively with elements of the binding pocket other than those observed for specificity-matched P1 side chains. The stereochemistry of the nucleophilic hydroxyl of Ser 195 in chymotrypsin relative to the scissile P1 bond of the inhibitors is identical to that observed for these groups in the trypsin-APPI complex, where Arg 15(I) is an optimal side chain for tryptic specificity. To further evaluate the diversity of sequences that can be accommodated by one of these inhibitors, APPI, we used phage display to randomly mutate residues 11, 13, 15, 17, and 19, which are major binding determinants. Inhibitors variants were selected that bound to either trypsin or chymotrypsin. As expected, trypsin specificity was principally directed by having a basic side chain at P1 (position 15); however, the P1 residues that were selected for chymotrypsin binding were His and Asn, rather than the expected large hydrophobic types. This can be rationalized by modeling these hydrophilic side chains to have similar H-bonding interactions to those observed in the structures of the described complexes. The specificity, or lack thereof, for the other individual subsites is discussed in the context of the "allowed" residues determined from a phage display mutagenesis selection experiment.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21053238 C.J.Farady, and C.S.Craik (2010).
Mechanisms of macromolecular protease inhibitors.
  Chembiochem, 11, 2341-2346.  
20226197 C.Li, M.Pazgier, C.Li, W.Yuan, M.Liu, G.Wei, W.Y.Lu, and W.Lu (2010).
Systematic mutational analysis of peptide inhibition of the p53-MDM2/MDMX interactions.
  J Mol Biol, 398, 200-213.
PDB code: 3lnz
20544968 D.J.Diller, C.Humblet, X.Zhang, and L.M.Westerhoff (2010).
Computational alanine scanning with linear scaling semiempirical quantum mechanical methods.
  Proteins, 78, 2329-2337.  
20696921 K.M.Dunse, Q.Kaas, R.F.Guarino, P.A.Barton, D.J.Craik, and M.A.Anderson (2010).
Molecular basis for the resistance of an insect chymotrypsin to a potato type II proteinase inhibitor.
  Proc Natl Acad Sci U S A, 107, 15016-15021.  
20800580 M.A.Qasim, J.Song, J.L.Markley, and M.Laskowski (2010).
Cleavage of peptide bonds bearing ionizable amino acids at P(1) by serine proteases with hydrophobic S(1) pocket.
  Biochem Biophys Res Commun, 400, 507-510.  
19920152 M.A.Salameh, J.L.Robinson, D.Navaneetham, D.Sinha, B.J.Madden, P.N.Walsh, and E.S.Radisky (2010).
The amyloid precursor protein/protease nexin 2 Kunitz inhibitor domain is a highly specific substrate of mesotrypsin.
  J Biol Chem, 285, 1939-1949.  
20008102 S.A.Assi, T.Tanaka, T.H.Rabbitts, and N.Fernandez-Fuentes (2010).
PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces.
  Nucleic Acids Res, 38, e86.  
20589642 S.Qin, and H.X.Zhou (2010).
Selection of near-native poses in CAPRI rounds 13-19.
  Proteins, 78, 3166-3173.  
18514224 C.J.Farady, P.F.Egea, E.L.Schneider, M.R.Darragh, and C.S.Craik (2008).
Structure of an Fab-protease complex reveals a highly specific non-canonical mechanism of inhibition.
  J Mol Biol, 380, 351-360.
PDB code: 3bn9
18217217 D.Dell'orco, and P.G.De Benedetti (2008).
Quantitative structure-activity relationship analysis of canonical inhibitors of serine proteases.
  J Comput Aided Mol Des, 22, 469-478.  
18286181 S.Macedo-Ribeiro, C.Almeida, B.M.Calisto, T.Friedrich, R.Mentele, J.Stürzebecher, P.Fuentes-Prior, and P.J.Pereira (2008).
Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick.
  PLoS ONE, 3, e1624.
PDB code: 2ody
17925020 A.Shulman-Peleg, M.Shatsky, R.Nussinov, and H.J.Wolfson (2007).
Spatial chemical conservation of hot spot interactions in protein-protein complexes.
  BMC Biol, 5, 43.  
17372355 M.Sherawat, P.Kaur, M.Perbandt, C.Betzel, W.A.Slusarchyk, G.S.Bisacchi, C.Chang, B.L.Jacobson, H.M.Einspahr, and T.P.Singh (2007).
Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 500-507.
PDB code: 2ayw
17976011 Y.González, T.Pons, J.Gil, V.Besada, M.Alonso-del-Rivero, A.S.Tanaka, M.S.Araujo, and M.A.Chávez (2007).
Characterization and comparative 3D modeling of CmPI-II, a novel 'non-classical' Kazal-type inhibitor from the marine snail Cenchritis muricatus (Mollusca).
  Biol Chem, 388, 1183-1194.  
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
  17597870 L.Li, B.Zhao, Z.Cui, J.Gan, M.K.Sakharkar, and P.Kangueane (2006).
Identification of hot spot residues at protein-protein interface.
  Bioinformation, 1, 121-126.  
15654893 N.Singh, T.Jabeen, S.Sharma, I.Roy, M.N.Gupta, S.Bilgrami, R.K.Somvanshi, S.Dey, M.Perbandt, C.Betzel, A.Srinivasan, and T.P.Singh (2005).
Detection of native peptides as potent inhibitors of enzymes. Crystal structure of the complex formed between treated bovine alpha-chymotrypsin and an autocatalytically produced fragment, IIe-Val-Asn-Gly-Glu-Glu-Ala-Val-Pro-Gly-Ser-Trp-Pro-Trp, at 2.2 angstroms resolution.
  FEBS J, 272, 562-572.
PDB code: 1oxg
15333934 C.Keil, R.Huber, W.Bode, and M.E.Than (2004).
Cloning, expression, crystallization and initial crystallographic analysis of the C-terminal domain of the amyloid precursor protein APP.
  Acta Crystallogr D Biol Crystallogr, 60, 1614-1617.  
12709070 A.Nagy, M.Trexler, and L.Patthy (2003).
Expression, purification and characterization of the second Kunitz-type protease inhibitor domain of the human WFIKKN protein.
  Eur J Biochem, 270, 2101-2107.  
12833568 F.Santamaria, Z.Wu, C.Boulègue, G.Pál, and W.Lu (2003).
Reexamination of the recognition preference of the specificity pocket of the Abl SH3 domain.
  J Mol Recognit, 16, 131-138.  
12483203 G.M.Süel, S.W.Lockless, M.A.Wall, and R.Ranganathan (2003).
Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
  Nat Struct Biol, 10, 59-69.  
12581670 M.Laskowski, M.A.Qasim, and Z.Yi (2003).
Additivity-based prediction of equilibrium constants for some protein-protein associations.
  Curr Opin Struct Biol, 13, 130-139.  
11910024 O.Buczek, K.Koscielska-Kasprzak, D.Krowarsch, M.Dadlez, and J.Otlewski (2002).
Analysis of serine proteinase-inhibitor interaction by alanine shaving.
  Protein Sci, 11, 806-819.  
11151003 M.L.Lamb, K.W.Burdick, S.Toba, M.M.Young, A.G.Skillman, X.Zou, J.R.Arnold, and I.D.Kuntz (2001).
Design, docking, and evaluation of multiple libraries against multiple targets.
  Proteins, 42, 296-318.  
11523096 V.J.Nesatyy (2001).
Gas-phase binding of non-covalent protein complexes between bovine pancreatic trypsin inhibitor and its target enzymes studied by electrospray ionization tandem mass spectrometry.
  J Mass Spectrom, 36, 950-959.  
11134922 W.R.Rypniewski, P.R.Ostergaard, M.Nørregaard-Madsen, M.Dauter, and K.S.Wilson (2001).
Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
  Acta Crystallogr D Biol Crystallogr, 57, 8.
PDB codes: 1fn8 1fy4 1fy5 1gdn 1gdq 1gdu
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.  
10064144 L.Kiczak, K.Koscielska, J.Otlewski, M.Czerwinski, and M.Dadlez (1999).
Phage display selection of P1 mutants of BPTI directed against five different serine proteinases.
  Biol Chem, 380, 101-105.  
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
10556568 Z.Malik, S.Amir, G.Pál, Z.Buzás, E.Várallyay, J.Antal, Z.Szilágyi, K.Vékey, B.Asbóth, A.Patthy, and L.Gráf (1999).
Proteinase inhibitors from desert locust, Schistocerca gregaria: engineering of both P(1) and P(1)' residues converts a potent chymotrypsin inhibitor to a potent trypsin inhibitor.
  Biochim Biophys Acta, 1434, 143-150.  
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.