PDBsum entry 5pad

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Hydrolase/hydrolase inhibitor PDB id
Protein chain
212 a.a. *
Waters ×30
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Binding of chloromethyl ketone substrate analogues to crysta papain
Structure: Papain. Chain: a. Engineered: yes. Phq-gly-phe-gly-chloromethylketone inhibitor. Chain: i. Synonym: zgpgck. Engineered: yes
Source: Carica papaya. Papaya. Organism_taxid: 3649. Tissue: fruit latex. Synthetic: yes
Biol. unit: Dimer (from PQS)
2.80Å     R-factor:   not given    
Authors: J.Drenth,K.H.Kalk,H.M.Swen
Key ref:
J.Drenth et al. (1976). Binding of chloromethyl ketone substrate analogues to crystalline papain. Biochemistry, 15, 3731-3738. PubMed id: 952885 DOI: 10.1021/bi00662a014
01-Nov-76     Release date:   12-Apr-77    
Supersedes: 6pap
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00784  (PAPA1_CARPA) -  Papain
345 a.a.
212 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Papain.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, with preference for a residue bearing a large hydrophobic sidechain at the P2 position. Does not accept Val at P1'.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     cysteine-type peptidase activity     1 term  


DOI no: 10.1021/bi00662a014 Biochemistry 15:3731-3738 (1976)
PubMed id: 952885  
Binding of chloromethyl ketone substrate analogues to crystalline papain.
J.Drenth, K.H.Kalk, H.M.Swen.
Papain (EC is a proteolytic enzyme, the three-dimensional structure of which has been determined by x-ray diffraction at 2.8 A resolution (Drenth, J., Jansonius, J.N., Koekoek, R., Swen, H. M., and Wothers, B.G. (1968), Nature (London) 218, 929-932). The active site is a groove on the molecular surface in which the essential sulfhydryl group of cysteine-25 is situated next to the imidazole ring of histidine-159. The main object of this study was to determine by the difference-Fourier technique the binding mode for the substrate in the groove in order to explain the substrate specificity of the enzyme (P2 should have a hydrophobic side chain (Berger and Schechter, 1970) and to contribute to an elucidation of the catalytic mechanism. To this end, three chloromethyl ketone substrate analogues were reacted with the enzyme by covalent attachment to the sulfur atom of cysteine-25. The products crystallized isomorphously with the parent structure that is not the native, active enzyme but a mixture of oxidized papain (probably papain-SO2-) and papain with an extra cysteine attached to cysteine-25. Although this made the interpretation of the difference electron density maps less easy, it provided us with a clear picture of the way in which the acyl part of the substrate binds in the active site groove. The carbonyl oxygen of the P1 residue is near two potential hydrogen-bond donating groups, the backbone NH of cysteine-25 and the NH2 of glutamine-19. Valine residues 133 and 157 are responsible for the preference of papain in its substrate splitting. By removing the methylene group that covalently attaches the inhibitor molecules to the sulfur atom of cysteine-25 we obtained acceptable models for the acyl-enzyme structure and for the tetrahedral intermediate. The carbonyl oxygen of the P1 residue, carrying a formal negative charge in the tetrahedral intermediate, is stabilized by formation of two hydrogen bonds with the backbone NH of cysteine-25 and the NH2 group of glutamine-19. This situation resembles that suggested for the proteolytic serine enzymes (Henderson, R., Wright, C. S., Hess, G. P., and Blow, D. M. (1971), Cold Spring Harbor Symp. Quant. Biol. 36, 63-70; Robertus, J. D., Kraut, J., Alden, R. A., and Birktoft, J. J. (1972b), Biochemistry 11, 4293-4303). The nitrogen atom of the scissile peptide bond was found close to the imidazole ring of histidine-159, suggesting a role for this ring in protonating the N atom of the leaving group (Lowe, 1970). This proton transfer would be facilitated by a 30 degrees rotation of the ring around the C beta-Cgamma bond from an in-plane position with the sulfur atom to an in-plane position with the N atom. The possibility of this rotation is derived from a difference electron-density map for fully oxidizied papain vs. the parent protein.

Literature references that cite this PDB file's key reference

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PDB codes: 3pse 3pt2
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Serine protease inhibitors N-alpha-tosyl-L-lysinyl-chloromethylketone (TLCK) and N-tosyl-L-phenylalaninyl-chloromethylketone (TPCK) do not inhibit caspase-3 and caspase-7 processing in cells exposed to pro-apoptotic inducing stimuli.
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PDB codes: 3bb7 3bba
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PDB code: 1iwd
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The lysosomal cysteine proteases.
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Inhibition of cysteine proteases by peptides containing aziridine-2,3-dicarboxylic acid building blocks.
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Crystal structure of porcine cathepsin H determined at 2.1 A resolution: location of the mini-chain C-terminal carboxyl group defines cathepsin H aminopeptidase function.
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PDB code: 8pch
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Crystal structure of human cathepsin S.
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PDB code: 1mem
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E-64 analogues as inhibitors of cathepsin B. On the role of the absolute configuration of the epoxysuccinyl group.
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Structure of recombinant human CPP32 in complex with the tetrapeptide acetyl-Asp-Val-Ala-Asp fluoromethyl ketone.
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PDB code: 1cp3
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Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution.
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PDB code: 1uch
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Adaptive amino acid replacements accompanied by domain fusion in reverse transcriptase.
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9158866 V.Martichonok, and J.B.Jones (1997).
Cysteine proteases such as papain are not inhibited by substrate analogue peptidyl boronic acids.
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  9165062 W.Baumeister, Z.Cejka, M.Kania, and E.Seemüller (1997).
The proteasome: a macromolecular assembly designed to confine proteolysis to a nanocompartment.
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Temporal and spatial control of the adenovirus proteinase by both a peptide and the viral DNA.
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A theoretical study of the active sites of papain and S195C rat trypsin: implications for the low reactivity of mutant serine proteinases.
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Structure of chymopapain at 1.7 A resolution.
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PDB code: 1yal
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Deacylation and reacylation for a series of acyl cysteine proteases, including acyl groups derived from novel chromophoric substrates.
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Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor.
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PDB code: 1avp
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The prosequence of procaricain forms an alpha-helical domain that prevents access to the substrate-binding cleft.
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PDB code: 1pci
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Bacterial aminopeptidases: properties and functions.
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The picornaviral 3C proteinases: cysteine nucleophiles in serine proteinase folds.
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Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design.
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PDB codes: 1cpj 1cte 1the
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Transglutaminase factor XIII uses proteinase-like catalytic triad to crosslink macromolecules.
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Anti-malarial drug development using models of enzyme structure.
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PDB code: 1huc
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Beta-lactamase of Bacillus licheniformis 749/C at 2 A resolution.
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PDB code: 2blm
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