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PDBsum entry 3prk
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protein ligands metals links
Hydrolase/hydrolase inhibitor PDB id
3prk

 

 

 

 

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Contents
Protein chain
279 a.a. *
Ligands
MSU-ALA-ALA-PRO-
ALV-0QE
Metals
_CA
Waters ×170
* Residue conservation analysis
PDB id:
3prk
Name: Hydrolase/hydrolase inhibitor
Title: Inhibition of proteinase k by methoxysuccinyl-ala-ala-pro-ala- chloromethyl ketone. An x-ray study at 2.2-angstroms resolution
Structure: Proteinase k. Chain: e. Engineered: yes. Methoxysuccinyl-ala-ala-pro-ala-chloromethyl ketone. Chain: i. Engineered: yes
Source: Engyodontium album. Organism_taxid: 37998. Tissue: limber. Gene: prok. Synthetic: yes
Biol. unit: Tetramer (from PQS)
Resolution:
2.20Å     R-factor:   0.198    
Authors: W.M.Wolf,J.Bajorath,A.Mueller,S.Raghunathan,T.P.Singh,W.Hinrichs, W.Saenger
Key ref: W.M.Wolf et al. (1991). Inhibition of proteinase K by methoxysuccinyl-Ala-Ala-Pro-Ala-chloromethyl ketone. An x-ray study at 2.2-A resolution. J Biol Chem, 266, 17695-17699. PubMed id: 1894649
Date:
07-Aug-91     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06873  (PRTK_PARAQ) -  Proteinase K from Parengyodontium album
Seq:
Struc: 		384 a.a.
279 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.64  - peptidase K.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of keratin and of other proteins, with subtilisin-like specificity. Hydrolyzes peptides amides.

 

 
J Biol Chem 266:17695-17699 (1991)
PubMed id: 1894649  
 
 
Inhibition of proteinase K by methoxysuccinyl-Ala-Ala-Pro-Ala-chloromethyl ketone. An x-ray study at 2.2-A resolution.
W.M.Wolf, J.Bajorath, A.Müller, S.Raghunathan, T.P.Singh, W.Hinrichs, W.Saenger.
 
  ABSTRACT  
 
The crystal structure of the transition state analog complex formed covalently between proteinase K and methoxysuccinyl-Ala-Ala-Pro-Ala-chloromethyl ketone was determined by x-ray diffraction methods at a resolution of 2.2 A and refined by constrained least squares to an R factor of 19.8% for the 11864 structure amplitudes greater than 1 sigma F. The chloromethyl ketone group is covalently linked with the active site functional groups His69(N epsilon) and Ser224(O gamma). The former has substituted for chlorine and the latter has attacked the carbon of the ketone group, thereby forming the tetrahedral carbon atom of the transition state analog. The peptide part of the inhibitor is in an extended conformation and fills subsites S1 to S5 of the substrate recognition site. Its backbone hydrogens bond with strands 100-104 and 132-136 of the substrate recognition site as the central strand of a three-stranded antiparallel beta-pleated sheet. This sheet formation is associated with a movement by approximately 1 A of strand 100-104 which is probably associated with the insertion of the bulky proline side chain. The methoxysuccinyl group is stacked on the phenolic side chain of Tyr104 that is a part of the bottom of the recognition site. Biochemical studies show that shorter inhibitors of this type are less effective than the longer one, because there are fewer hydrogen bonding and van der Waals/stacking interactions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20446009 S.Q.Liu, Y.Tao, Z.H.Meng, Y.X.Fu, and K.Q.Zhang (2011).
The effect of calciums on molecular motions of proteinase K.
  J Mol Model, 17, 289-300.  
  19255481 F.Ye, L.Liang, Q.Mi, J.Yang, Z.Lou, Y.Sun, Y.Guo, Z.Meng, and K.Zhang (2009).
Preliminary crystallographic study of two cuticle-degrading proteases from the nematophagous fungi Lecanicillium psalliotae and Paecilomyces lilacinus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 271-274.  
  19255463 S.B.Larson, J.S.Day, C.Nguyen, R.Cudney, and A.McPherson (2009).
High-resolution structure of proteinase K cocrystallized with digalacturonic acid.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 192-198.
PDB code: 3dyb
17511867 S.Q.Liu, Z.H.Meng, J.K.Yang, Y.X.Fu, and K.Q.Zhang (2007).
Characterizing structural features of cuticle-degrading proteases from fungi by molecular modeling.
  BMC Struct Biol, 7, 33.  
16367748 R.Helland, A.N.Larsen, A.O.Smalås, and N.P.Willassen (2006).
The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species.
  FEBS J, 273, 61-71.
PDB code: 2b6n
11258922 C.Betzel, S.Gourinath, P.Kumar, P.Kaur, M.Perbandt, S.Eschenburg, and T.P.Singh (2001).
Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 A resolution.
  Biochemistry, 40, 3080-3088.
PDB code: 1ic6
10393299 J.M.Harp, B.L.Hanson, D.E.Timm, and G.J.Bunick (1999).
Macromolecular crystal annealing: evaluation of techniques and variables.
  Acta Crystallogr D Biol Crystallogr, 55, 1329-1334.  
  8976553 A.K.Saxena, T.P.Singh, K.Peters, S.Fittkau, and C.Betzel (1996).
Strategy to design peptide inhibitors: structure of a complex of proteinase K with a designed octapeptide inhibitor N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2 at 2.5 A resolution.
  Protein Sci, 5, 2453-2458.
PDB code: 1pfg
8022970 M.J.Zvelebil, and J.M.Thornton (1993).
Peptide-protein interactions: an overview.
  Q Rev Biophys, 26, 333-363.  
1396684 B.Dahlmann, L.Kuehn, A.Grziwa, P.Zwickl, and W.Baumeister (1992).
Biochemical properties of the proteasome from Thermoplasma acidophilum.
  Eur J Biochem, 208, 789-797.  
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.

 

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