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PDBsum entry 2prk
Go to PDB code: 
protein metals links
Serine proteinase PDB id
2prk

 

 

 

 

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Contents
Protein chain
279 a.a. *
Metals
_CA ×2
Waters ×178
* Residue conservation analysis
PDB id:
2prk
Name: Serine proteinase
Title: Synchrotron x-ray data collection and restrained least-squares refinement of the crystal structure of proteinase k at 1.5 angstroms resolution
Structure: Proteinase k. Chain: a. Engineered: yes
Source: Engyodontium album. Organism_taxid: 37998
Resolution:
1.50Å     R-factor:   0.167    
Authors: C.Betzel,G.P.Pal,W.Saenger
Key ref: C.Betzel et al. (1988). Synchrotron X-ray data collection and restrained least-squares refinement of the crystal structure of proteinase K at 1.5 A resolution. Acta Crystallogr B, 44, 163-172. PubMed id: 3271105
Date:
30-Nov-87     Release date:   16-Apr-88    
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.

 

 
Acta Crystallogr B 44:163-172 (1988)
PubMed id: 3271105  
 
 
Synchrotron X-ray data collection and restrained least-squares refinement of the crystal structure of proteinase K at 1.5 A resolution.
C.Betzel, G.P.Pal, W.Saenger.
 
  ABSTRACT  
 
The structure of the serine endopeptidase proteinase K (279 amino acid residues; 28,790 daltons) has been refined by restrained least-squares methods to a conventional R value of 16.7% employing synchrotron film data of 30,812 reflections greater than 3 sigma in the 5.0 to 1.5 A resolution range. During refinement, the molecular structure was restrained to known stereochemistry, with root-mean-square (r.m.s.) deviation of 0.015 A from ideal bond lengths. The average atomic temperature factor, B, is 11.1 A2 for all atoms. The final model comprises 2020 protein atoms and 174 solvent molecules (which were given unit occupancies). Four corrections to the amino acid sequence were made, which were confirmed later by sequence analysis of the proteinase K gene: a deletion of one glycine in position 80; a change of sequence in position 207-208 and insertions of the dipeptide 210-211 and of residue 270. The r.m.s. deviation in the alpha-C atomic positions between the final refined model and the initial model built on the basis of a 3.3 A mini-map is 1.72 A for 227 out of 266 residues, which were originally traced in the mini-map without sequence information. The positions of the remaining 39 residues deviate by more than 8 A from the original ones and are located in regions where extensive revision of the structural model was necessary.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19937325 R.C.Cheng, and B.S.Zhorov (2010).
Docking of calcium ions in proteins with flexible side chains and deformable backbones.
  Eur Biophys J, 39, 825-838.  
  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
17502100 D.E.Piper, S.Jackson, Q.Liu, W.G.Romanow, S.Shetterly, S.T.Thibault, B.Shan, and N.P.Walker (2007).
The crystal structure of PCSK9: a regulator of plasma LDL-cholesterol.
  Structure, 15, 545-552.
PDB code: 2pmw
11856298 O.L.Franco, D.J.Rigden, F.R.Melo, and M.F.Grossi-De-Sá (2002).
Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases.
  Eur J Biochem, 269, 397-412.  
9115441 J.R.Martin, F.A.Mulder, Y.Karimi-Nejad, J.van der Zwan, M.Mariani, D.Schipper, and R.Boelens (1997).
The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site.
  Structure, 5, 521-532.
PDB code: 1ah2
  8061606 D.Fischer, H.Wolfson, S.L.Lin, and R.Nussinov (1994).
Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding.
  Protein Sci, 3, 769-778.  
  1303752 M.E.Karpen, P.L.de Haseth, and K.E.Neet (1992).
Differences in the amino acid distributions of 3(10)-helices and alpha-helices.
  Protein Sci, 1, 1333-1342.  
2077361 B.B.Samal, B.Karan, T.C.Boone, T.D.Osslund, K.K.Chen, and Y.Stabinsky (1990).
Isolation and characterization of the gene encoding a novel, thermostable serine proteinase from the mould Tritirachium album Limber.
  Mol Microbiol, 4, 1789-1792.  
3203685 C.Betzel, G.P.Pal, and W.Saenger (1988).
Three-dimensional structure of proteinase K at 0.15-nm resolution.
  Eur J Biochem, 178, 155-171.  
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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