spacer
spacer

PDBsum entry 1pek
Go to PDB code: 
protein ligands links
Hydrolase/hydrolase inhibitor PDB id
1pek

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
279 a.a. *
Ligands
PRO-ALA-PRO-PHE
DAL-ALA
Waters ×188
* Residue conservation analysis
PDB id:
1pek
Name: Hydrolase/hydrolase inhibitor
Title: Structure of the complex of proteinase k with a substrate-analogue hexa-peptide inhibitor at 2.2 angstroms resolution
Structure: Proteinase k. Chain: e. Peptide pro-ala-pro-phe. Chain: c. Engineered: yes. Other_details: the complete peptide is n-ac-pro-ala-pro-phe-d-ala- ala-nh2 and is hydrolysed and represented as chains c and d. D-dal-ala-nh2. Chain: d.
Source: Tritirachium album. Engyodontium album. Organism_taxid: 37998. Synthetic: yes. Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.165    
Authors: C.Betzel,T.P.Singh,M.Visanji,K.Peters,S.Fittkau,W.Saenger,K.S.Wilson
Key ref: C.Betzel et al. (1993). Structure of the complex of proteinase K with a substrate analogue hexapeptide inhibitor at 2.2-A resolution. J Biol Chem, 268, 15854-15858. PubMed id: 8340410
Date:
19-Jan-93     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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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 268:15854-15858 (1993)
PubMed id: 8340410  
 
 
Structure of the complex of proteinase K with a substrate analogue hexapeptide inhibitor at 2.2-A resolution.
C.Betzel, T.P.Singh, M.Visanji, K.Peters, S.Fittkau, W.Saenger, K.S.Wilson.
 
  ABSTRACT  
 
The crystal structure of a transition state/product complex formed by the interaction between proteinase K and the substrate analogue N-Ac-L-Pro-L-Ala-L-Pro-L-Phe-D-Ala-L-Ala-NH2 has been determined at a resolution of 2.2 A and refined to an R-factor of 0.165 for 12,725 reflections. The inhibitor forms a stable complex through a series of hydrogen bonds with protein atoms and water molecules. The inhibitor is hydrolyzed between Phe 4I and D-Ala5I (I indicates inhibitor). The two fragments are separated by a distance of 3.07 A between the carbonyl carbon and the main chain nitrogen. Both fragments remain bound to the protein. The N-terminal fragment occupies subsites S5 to S1, whereas the C-terminal part is bound in S1' and S2', the first time that electron density for a substrate analogue has been observed in the P1' and P2' sites of a subtilisin-like enzyme. The flexible segments of the substrate recognition sites Gly100-Tyr104 and Ser132-Gly136 move appreciably to accommodate the inhibitor. Biochemical results indicate an inhibition by this specifically designed peptide of 95%.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20066306 M.A.Saeed, F.R.Fronczek, M.J.Huang, and M.Alamgir Hossain (2010).
Unusual bridging of three nitrates with two bridgehead protons in an octaprotonated azacryptand.
  Chem Commun (Camb), 46, 404-406.  
  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
11969409 P.Ingallinella, D.Fattori, S.Altamura, C.Steinkühler, U.Koch, D.Cicero, R.Bazzo, R.Cortese, E.Bianchi, and A.Pessi (2002).
Prime site binding inhibitors of a serine protease: NS3/4A of hepatitis C virus.
  Biochemistry, 41, 5483-5492.  
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
11041854 P.Ingallinella, E.Bianchi, R.Ingenito, U.Koch, C.Steinkühler, S.Altamura, and A.Pessi (2000).
Optimization of the P'-region of peptide inhibitors of hepatitis C virus NS3/4A protease.
  Biochemistry, 39, 12898-12906.  
  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
  7795518 J.J.Perona, and C.S.Craik (1995).
Structural basis of substrate specificity in the serine proteases.
  Protein Sci, 4, 337-360.
PDB code: 1amh
8020465 R.J.Siezen, J.W.Creemers, and W.J.Van de Ven (1994).
Homology modelling of the catalytic domain of human furin. A model for the eukaryotic subtilisin-like proprotein convertases.
  Eur J Biochem, 222, 255-266.  
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.

 

spacer
spacer