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Hydrolase PDB id
1meg
Jmol
Contents
Protein chain
216 a.a. *
Ligands
E64
EOH
Waters ×94
* Residue conservation analysis
PDB id:
1meg
Name: Hydrolase
Title: Crystal structure of a caricain d158e mutant in complex with e-64
Structure: Caricain. Chain: a. Synonym: papaya proteinase, protease omega. Engineered: yes. Mutation: yes
Source: Carica papaya. Papaya. Organism_taxid: 3649. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PDB file)
Resolution:
2.00Å     R-factor:   0.193    
Authors: N.A.Katerelos
Key ref: N.A.Katerelos et al. (1996). Crystal structure of a caricain D158E mutant in complex with E-64. FEBS Lett, 392, 35-39. PubMed id: 8769310 DOI: 10.1016/0014-5793(96)00697-7
Date:
04-May-96     Release date:   11-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10056  (PAPA3_CARPA) -  Caricain
Seq:
Struc: 		348 a.a.
216 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.3.4.22.30  - Caricain.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, similar to those of papain and chymopapain.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     cysteine-type peptidase activity     2 terms  

 

 
DOI no: 10.1016/0014-5793(96)00697-7 FEBS Lett 392:35-39 (1996)
PubMed id: 8769310  
 
 
Crystal structure of a caricain D158E mutant in complex with E-64.
N.A.Katerelos, M.A.Taylor, M.Scott, P.W.Goodenough, R.W.Pickersgill.
 
  ABSTRACT  
 
The structure of the D158E mutant of caricain (previously known as papaya protease omega) in complex with E-64 has been determined at 2.0 A resolution (overall R factor 19.3%). The structure reveals that the substituted glutamate makes the same pattern of hydrogen bonds as the aspartate in native caricain. This was not anticipated since in the native structure there is insufficient room to accommodate the glutamate side chain. The glutamate is accommodated in the mutant by a local expansion of the structure demonstrating that small structural changes are responsible for the change in activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19430116 T.K.Nandi, H.R.Bairagya, B.P.Mukhopadhyay, K.Sekar, D.Sukul, and A.K.Bera (2009).
Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease.
  J Biosci, 34, 27-34.  
  18540057 M.T.Gomes, R.D.Teixeira, H.d.e. .A.Ribeiro, A.P.Turchetti, C.F.Junqueira, M.T.Lopes, C.E.Salas, and R.A.Nagem (2008).
Purification, crystallization and preliminary X-ray analysis of CMS1MS2: a cysteine proteinase from Carica candamarcensis latex.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 492-494.  
17452780 J.A.Gavira, L.A.González-Ramírez, M.C.Oliver-Salvador, M.Soriano-García, and J.M.García-Ruiz (2007).
Structure of the mexicain-E-64 complex and comparison with other cysteine proteases of the papain family.
  Acta Crystallogr D Biol Crystallogr, 63, 555-563.  
16149114 C.Drahl, B.F.Cravatt, and E.J.Sorensen (2005).
Protein-reactive natural products.
  Angew Chem Int Ed Engl, 44, 5788-5809.  
16231289 H.Li, A.D.Robertson, and J.H.Jensen (2005).
Very fast empirical prediction and rationalization of protein pKa values.
  Proteins, 61, 704-721.  
16283547 W.Liu, W.Ye, Z.Wang, H.Chao, and J.Lian (2005).
Preparation and characterization of a truncated caricain lacking 41 residues from the N-terminal.
  Protein J, 24, 243-251.  
15502326 M.C.Oliver-Salvador, L.A.González-Ramírez, J.A.Gavira, M.Soriano-García, and J.M.García-Ruiz (2004).
Purification, crystallization and preliminary X-ray analysis of mexicain.
  Acta Crystallogr D Biol Crystallogr, 60, 2058-2060.  
  14725770 Y.Zong, S.K.Mazmanian, O.Schneewind, and S.V.Narayana (2004).
The structure of sortase B, a cysteine transpeptidase that tethers surface protein to the Staphylococcus aureus cell wall.
  Structure, 12, 105-112.
PDB codes: 1qwz 1qx6 1qxa
11602025 S.Bhattacharya, S.Ghosh, S.Chakraborty, A.K.Bera, B.P.Mukhopadhayay, I.Dey, and A.Banerjee (2001).
Insight to structural subsite recognition in plant thiol protease-inhibitor complexes : understanding the basis of differential inhibition and the role of water.
  BMC Struct Biol, 1, 4.  
10998237 C.E.Carter, H.Marriage, and P.W.Goodenough (2000).
Mutagenesis and kinetic studies of a plant cysteine proteinase with an unusual arrangement of acidic amino acids in and around the active site.
  Biochemistry, 39, 11005-11013.  
10350606 C.Czaplewski, Z.Grzonka, M.Jaskólski, F.Kasprzykowski, M.Kozak, E.Politowska, and J.Ciarkowski (1999).
Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
  Biochim Biophys Acta, 1431, 290-305.  
10380357 K.Matsumoto, K.Mizoue, K.Kitamura, W.C.Tse, C.P.Huber, and T.Ishida (1999).
Structural basis of inhibition of cysteine proteases by E-64 and its derivatives.
  Biopolymers, 51, 99.  
10410800 M.E.McGrath (1999).
The lysosomal cysteine proteases.
  Annu Rev Biophys Biomol Struct, 28, 181-204.  
  9524065 D.Turk, G.Guncar, M.Podobnik, and B.Turk (1998).
Revised definition of substrate binding sites of papain-like cysteine proteases.
  Biol Chem, 379, 137-147.  
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.