1BJR

COMPLEX FORMED BETWEEN PROTEOLYTICALLY GENERATED LACTOFERRIN FRAGMENT AND PROTEINASE K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K.

Singh, T.P.Sharma, S.Karthikeyan, S.Betzel, C.Bhatia, K.L.

(1998) Proteins 33: 30-38


  • PubMed Abstract: 
  • Lactoferrin is an iron binding glycoprotein with a molecular weight of 80 kDa. The molecule is divided into two lobes representing the N-terminal and C-terminal halves of the polypeptide chain, each containing an iron binding site. The serine protein ...

    Lactoferrin is an iron binding glycoprotein with a molecular weight of 80 kDa. The molecule is divided into two lobes representing the N-terminal and C-terminal halves of the polypeptide chain, each containing an iron binding site. The serine proteinases such as trypsin, chymotrypsin, and pepsin hydrolyze lactoferrin into two unequal halves while proteinase K divides this protein into two equal halves. In the first step of hydrolysis by proteinase K, the C- and N-lobes, each having a molecular weight of approximately 40 kDa, are generated. In the next step, the lobes are further hydrolyzed into small molecular weight peptides. The proteinase K isolated from the hydrolyzed product does not show enzymatic activity suggesting that the enzyme is inhibited. Furthermore, the hydrolysis experiments on N-lobe and C-lobe showed that the inhibitory fragment came from the C-lobe. The purified lactoferrin fragment was found to be a decapeptide with an amino acid sequence of H2N-Val-Ala-Gln-Gly-Ala-Ala-Gly-Leu-Ala-COOH. The complex formed between proteinase K and lactoferrin fragment was crystallized by microdialysis. The crystals belonged to the monoclinic space group P2(1) with cell dimensions a = 44.4 A, b = 38.6 A, c = 79.2 A, beta = 105.8 degrees and Z = 2. The crystal structure has been determined at 2.4 A resolution. It has been refined to an R factor of 0.163 for 9044 reflections. The Lf-fragment forms several intermolecular interactions with proteinase K. The Ser-224 Ogamma and His-57 N epsilon2 move away to a distance of 3.68 A in the complex. In the crystal structure, Gln-3I (I indicates inhibitor i.e., lactoferrin fragment) is involved in a direct intermolecular interaction with a symmetry related proteinase K molecule through a strong hydrogen bond with Asp-254. The mode of intermolecular interactions in the complex conformational features of the enzyme and placement of the fragment with respect to the enzyme resemble with the molecular complex of proteinase K with its natural inhibitor PKI3 from wheat.


    Related Citations: 
    • Synchrotron X-Ray Data Collection and Restrained Least-Squares Refinement of the Crystal Structure of Proteinase K at 1.5 A Resolution
      Betzel, C.,Pal, G.P.,Saenger, W.
      (1988) Acta Crystallogr.,Sect.B 44: 163
    • Inhibition of Proteinase K by Methoxysuccinyl-Ala-Ala-Pro-Ala-Chloromethyl Ketone. An X-Ray Study at 2.2-A Resolution
      Wolf, W.M.,Bajorath, J.,Muller, A.,Raghunathan, S.,Singh, T.P.,Hinrichs, W.,Saenger, W.
      (1991) J.Biol.Chem. 266: 17695


    Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi. tps@medinst.ernet.in




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEINASE K
E
279Engyodontium albumGene Names: PROK
EC: 3.4.21.64
Find proteins for P06873 (Engyodontium album)
Go to UniProtKB:  P06873
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LACTOFERRIN
I
10N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.600α = 90.00
b = 38.581β = 105.80
c = 79.220γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
CCP4refinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance