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Hydrolase (acid proteinase) PDB id
4pep
Jmol
Contents
Protein chain
326 a.a. *
Waters ×187
* Residue conservation analysis
PDB id:
4pep
Name: Hydrolase (acid proteinase)
Title: The molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 angstroms resolution
Structure: Pepsin. Chain: a. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823
Resolution:
1.80Å     R-factor:   0.174    
Authors: N.Andreeva,A.A.Fedorov,A.Sielecki,M.James
Key ref: A.R.Sielecki et al. (1990). Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution. J Mol Biol, 214, 143-170. PubMed id: 2115087 DOI: 10.1016/0022-2836(90)90153-D
Date:
18-Dec-89     Release date:   15-Apr-90    
Supersedes: 1pep
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00791  (PEPA_PIG) -  Pepsin A
Seq:
Struc: 		385 a.a.
326 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.4.23.1  - Pepsin A.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1' positions. Cleaves 1-Phe-|-Val-2, 4-Gln-|-His-5, 13-Glu-|- Ala-14, 14-Ala-|-Leu-15, 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17, 23-Gly-|- Phe-24, 24-Phe-|-Phe-25 and 25-Phe-|-Tyr-26 bonds in the B chain of insulin.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     aspartic-type endopeptidase activity     1 term  

 

 
DOI no: 10.1016/0022-2836(90)90153-D J Mol Biol 214:143-170 (1990)
PubMed id: 2115087  
 
 
Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution.
A.R.Sielecki, A.A.Fedorov, A.Boodhoo, N.S.Andreeva, M.N.James.
 
  ABSTRACT  
 
The molecular structure of the archetypal aspartic proteinase, porcine pepsin (EC 3.4.23.1), has been refined using data collected from a single monoclinic crystal on a twin multiwire detector system to 1.8 A resolution. The current crystallographic R-factor (= sigma parallel to Fo/-/Fc parallel to/sigma/Fo/) is 0.174 for the 20,519 reflections with /Fo/ greater than or equal to 3 sigma (Fo) in the range 8.0 to 1.8 A (/Fo/ and /Fc/ are the observed and calculated structure factor amplitudes respectively). The refinement has shown conclusively that there are only 326 amino acid residues in porcine pepsin. Ile230 is not present in the molecule. The two catalytic residues Asp32 and Asp215 have dispositions in porcine pepsin very similar to the dispositions of the equivalent residues in the other aspartic proteinases of known structure. A bound solvent molecule is associated with both carboxyl groups at the active site. No bound ethanol molecule could be identified conclusively in the structure. The average thermal motion parameter of the residues that comprise the C-terminal domain of pepsin is approximately twice that of the residues in the N-terminal domain. Comparisons of the tertiary structure of pepsin with porcine pepsinogen, penicillopepsin, rhizopus pepsin and endothia pepsin reveal that the N-terminal domains are topographically more similar than the conformationally flexible C-terminal domains. The conformational differences may be modeled as rigid-body movements of "reduced" C-terminal domains (residues 193 to 212 and 223 to 298 in pepsin numbering). A similar movement of the C-terminal domain of endothia pepsin has been observed upon inhibitor binding. A phosphoryl group covalently attached to Ser68 O gamma has been identified in the electron density map of porcine pepsin. The low pKa1 value for this group, coupled with unusual microenvironments for several of the aspartyl carboxylate groups, ensures a net negative charge on porcine pepsin in a strongly acid medium. Thus, there is a structural explanation for the very early observations of "anodic migration" of porcine pepsin at pH 1. In the crystals, the molecules are packed tightly into a monoclinic unit cell. There are 190 direct contacts (less than or equal to 4.0 A) between a central pepsin molecule and the five unique symmetry-related molecules surrounding it in the crystalline lattice. The tight packing in this cell makes pepsin's active site and binding cleft relatively inaccessible to substrate analogs or inhibitors.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB codes: 3qrv 3qs1
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PDB code: 3f9q
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Crystal structure of a dimerized cockroach allergen Bla g 2 complexed with a monoclonal antibody.
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PDB code: 2nr6
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PDB codes: 2h6s 2h6t
17976195 S.Brier, G.Maria, V.Carginale, A.Capasso, Y.Wu, R.M.Taylor, N.B.Borotto, C.Capasso, and J.R.Engen (2007).
Purification and characterization of pepsins A1 and A2 from the Antarctic rock cod Trematomus bernacchii.
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15585673 A.Maheshwari, W.Lu, W.C.Guida, R.D.Christensen, and D.A.Calhoun (2005).
IL-8/CXC ligand 8 survives neonatal gastric digestion as a result of intrinsic aspartyl proteinase resistance.
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12944303 G.Giraud, J.Karolin, and K.Wynne (2003).
Low-frequency modes of peptides and globular proteins in solution observed by ultrafast OHD-RIKES spectroscopy.
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12649430 Y.O.Kamatari, C.M.Dobson, and T.Konno (2003).
Structural dissection of alkaline-denatured pepsin.
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11679720 F.Canduri, L.G.Teodoro, V.Fadel, C.C.Lorenzi, V.Hial, R.A.Gomes, J.R.Neto, and W.F.de Azevedo (2001).
Structure of human uropepsin at 2.45 A resolution.
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PDB code: 1flh
11438724 L.Wang, Y.Pang, T.Holder, J.R.Brender, A.V.Kurochkin, and E.R.Zuiderweg (2001).
Functional dynamics in the active site of the ribonuclease binase.
  Proc Natl Acad Sci U S A, 98, 7684-7689.  
11714911 N.S.Andreeva, and L.D.Rumsh (2001).
Analysis of crystal structures of aspartic proteinases: on the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes.
  Protein Sci, 10, 2439-2450.  
11168403 S.Fujiwara, S.Kunugi, H.Oyama, and K.Oda (2001).
Effects of pressure on the activity and spectroscopic properties of carboxyl proteinases. Apparent correlation of pepstatin-insensitivity and pressure response.
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11418762 S.W.Cho, N.Kim, M.U.Choi, and W.Shin (2001).
Structure of aspergillopepsin I from Aspergillus phoenicis: variations of the S1'-S2 subsite in aspartic proteinases.
  Acta Crystallogr D Biol Crystallogr, 57, 948-956.
PDB code: 1ibq
11021803 L.Hong, G.Koelsch, X.Lin, S.Wu, S.Terzyan, A.K.Ghosh, X.C.Zhang, and J.Tang (2000).
Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor.
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PDB code: 1fkn
10713513 M.Fujinaga, M.M.Cherney, N.I.Tarasova, P.A.Bartlett, J.E.Hanson, and M.N.James (2000).
Structural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog.
  Acta Crystallogr D Biol Crystallogr, 56, 272-279.
PDB code: 1qrp
10747810 T.Konno, Y.O.Kamatari, N.Tanaka, H.Kamikubo, C.M.Dobson, and K.Nagayama (2000).
A partially unfolded structure of the alkaline-denatured state of pepsin and its implication for stability of the zymogen-derived protein.
  Biochemistry, 39, 4182-4190.  
10488111 C.Frazão, I.Bento, J.Costa, C.M.Soares, P.Veríssimo, C.Faro, E.Pires, J.Cooper, and M.A.Carrondo (1999).
Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp-containing aspartic proteinase from the flowers of Cynara cardunculus L.
  J Biol Chem, 274, 27694-27701.
PDB code: 1b5f
10215892 C.Richter, T.Tanaka, T.Koseki, and R.Y.Yada (1999).
Contribution of a prosegment lysine residue to the function and structure of porcine pepsinogen A and its active form pepsin A.
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10089458 J.Yang, and J.W.Quail (1999).
Structure of the Rhizomucor miehei aspartic proteinase complexed with the inhibitor pepstatin A at 2.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 625-630.
PDB code: 2rmp
9694859 J.W.Cuozzo, K.Tao, M.Cygler, J.S.Mort, and G.G.Sahagian (1998).
Lysine-based structure responsible for selective mannose phosphorylation of cathepsin D and cathepsin L defines a common structural motif for lysosomal enzyme targeting.
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9485411 R.B.Rose, C.S.Craik, and R.M.Stroud (1998).
Domain flexibility in retroviral proteases: structural implications for drug resistant mutations.
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PDB code: 1az5
9761815 S.Karlsen, E.Hough, and R.L.Olsen (1998).
Structure and proposed amino-acid sequence of a pepsin from atlantic cod (Gadus morhua).
  Acta Crystallogr D Biol Crystallogr, 54, 32-46.
PDB code: 1am5
9363769 D.Arnold, W.Keilholz, H.Schild, T.Dumrese, S.Stevanović, and H.G.Rammensee (1997).
Substrate specificity of cathepsins D and E determined by N-terminal and C-terminal sequencing of peptide pools.
  Eur J Biochem, 249, 171-179.  
9335526 J.Symersky, M.Monod, and S.I.Foundling (1997).
High-resolution structure of the extracellular aspartic proteinase from Candida tropicalis yeast.
  Biochemistry, 36, 12700-12710.
PDB code: 1j71
9405415 K.Aoki, H.Taguchi, Y.Shindo, M.Yoshida, K.Ogasahara, K.Yutani, and N.Tanaka (1997).
Calorimetric observation of a GroEL-protein binding reaction with little contribution of hydrophobic interaction.
  J Biol Chem, 272, 32158-32162.  
9228062 T.Shintani, K.Nomura, and E.Ichishima (1997).
Engineering of porcine pepsin. Alteration of S1 substrate specificity of pepsin to those of fungal aspartic proteinases by site-directed mutagenesis.
  J Biol Chem, 272, 18855-18861.  
  8845753 C.Abad-Zapatero, R.Goldman, S.W.Muchmore, C.Hutchins, K.Stewart, J.Navaza, C.D.Payne, and T.L.Ray (1996).
Structure of a secreted aspartic protease from C. albicans complexed with a potent inhibitor: implications for the design of antifungal agents.
  Protein Sci, 5, 640-652.
PDB code: 1zap
  8673731 G.Houen, M.T.Madsen, K.W.Harlow, P.Lønblad, and B.Foltmann (1996).
The primary structure and enzymic properties of porcine prochymosin and chymosin.
  Int J Biochem Cell Biol, 28, 667-675.  
8913621 G.Iliadis, B.Brzezinski, and G.Zundel (1996).
Aspartic proteinases: Fourier transform infrared spectroscopic studies of a model of the active side.
  Biophys J, 71, 2840-2847.  
8841139 R.B.Rose, C.S.Craik, N.L.Douglas, and R.M.Stroud (1996).
Three-dimensional structures of HIV-1 and SIV protease product complexes.
  Biochemistry, 35, 12933-12944.
PDB codes: 1ytg 1yth 1yti 1ytj
  7663352 M.Fujinaga, M.M.Chernaia, N.I.Tarasova, S.C.Mosimann, and M.N.James (1995).
Crystal structure of human pepsin and its complex with pepstatin.
  Protein Sci, 4, 960-972.
PDB codes: 1psn 1pso
7642580 T.Kageyama, M.Ichinose, and S.Yonezawa (1995).
Processing of the precursors to neurotensin and other bioactive peptides by cathepsin E.
  J Biol Chem, 270, 19135-19140.  
8143488 M.S.Johnson, N.Srinivasan, R.Sowdhamini, and T.L.Blundell (1994).
Knowledge-based protein modeling.
  Crit Rev Biochem Mol Biol, 29, 1.  
7828434 S.S.Twining (1994).
Regulation of proteolytic activity in tissues.
  Crit Rev Biochem Mol Biol, 29, 315-383.  
8393577 E.T.Baldwin, T.N.Bhat, S.Gulnik, M.V.Hosur, R.C.Sowder, R.E.Cachau, J.Collins, A.M.Silva, and J.W.Erickson (1993).
Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design.
  Proc Natl Acad Sci U S A, 90, 6796-6800.
PDB codes: 1lya 1lyb
  8467789 P.Metcalf, and M.Fusek (1993).
Two crystal structures for cathepsin D: the lysosomal targeting signal and active site.
  EMBO J, 12, 1293-1302.  
8259000 S.S.Abdel-Meguid (1993).
Inhibitors of aspartyl proteinases.
  Med Res Rev, 13, 731-778.  
8404890 T.Kageyama (1993).
Rabbit procathepsin E and cathepsin E. Nucleotide sequence of cDNA, hydrolytic specificity for biologically active peptides and gene expression during development.
  Eur J Biochem, 216, 717-728.  
  8401224 X.Lin, J.A.Loy, F.Sussman, and J.Tang (1993).
Conformational instability of the N- and C-terminal lobes of porcine pepsin in neutral and alkaline solutions.
  Protein Sci, 2, 1383-1390.  
  1304340 B.Veerapandian, J.B.Cooper, A.Sali, T.L.Blundell, R.L.Rosati, B.W.Dominy, D.B.Damon, and D.J.Hoover (1992).
Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases.
  Protein Sci, 1, 322-328.
PDB code: 1epo
1594574 J.A.Hartsuck, G.Koelsch, and S.J.Remington (1992).
The high-resolution crystal structure of porcine pepsinogen.
  Proteins, 13, 1.
PDB code: 3psg
  1710977 A.Volbeda, A.Lahm, F.Sakiyama, and D.Suck (1991).
Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.
  EMBO J, 10, 1607-1618.  
1935977 T.Kageyama, K.Tanabe, and O.Koiwai (1991).
Development-dependent expression of isozymogens of monkey pepsinogens and structural differences between them.
  Eur J Biochem, 202, 205-215.  
17203064 , (0).
  , 0, 0.  
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