4XOJ

Structure of bovine trypsin in complex with analogues of sunflower inhibitor 1 (SFTI-1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.91 Å
  • R-Value Free: 0.114 
  • R-Value Work: 0.103 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Investigation of Serine-Proteinase-Catalyzed Peptide Splicing in Analogues of Sunflower Trypsin Inhibitor 1 (SFTI-1).

Karna, N.Legowska, A.Malicki, S.Debowski, D.Golik, P.Gitlin, A.Grudnik, P.Wladyka, B.Brzozowski, K.Dubin, G.Rolka, K.

(2015) Chembiochem 16: 2036-2045

  • DOI: 10.1002/cbic.201500296

  • PubMed Abstract: 
  • Serine-proteinase-catalyzed peptide splicing was demonstrated in analogues of the trypsin inhibitor SFTI-1: both single peptides and two-peptide chains (C- and N-terminal peptide chains linked by a disulfide bridge). In the second series, peptide spl ...

    Serine-proteinase-catalyzed peptide splicing was demonstrated in analogues of the trypsin inhibitor SFTI-1: both single peptides and two-peptide chains (C- and N-terminal peptide chains linked by a disulfide bridge). In the second series, peptide splicing with catalytic amount of proteinase was observed only when formation of acyl-enzyme intermediate was preceded by hydrolysis of the substrate Lys-Ser peptide bond. Here we demonstrate that with an equimolar amount of the proteinase, splicing occurs in all the two-peptide-chain analogues. This conclusion was supported by high resolution crystal structures of selected analogues in complex with trypsin. We showed that the process followed a direct transpeptidation mechanism. Thus, the acyl-enzyme intermediate was formed and was immediately used for a new peptide bond formation; products associated with the hydrolysis of the acyl-enzyme were not observed. The peptide splicing was sequence- not structure-specific.


    Organizational Affiliation

    Malopolska Centre of Biotechnology, Jagiellonian Univeristy, Gronostajowa 7a, 30-387, Krakow, Poland.,Department of Bioorganic Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A
246Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trypsin inhibitor 1
B
13Helianthus annuusMutation(s): 0 
Gene Names: sfti1
Find proteins for Q4GWU5 (Helianthus annuus)
Go to UniProtKB:  Q4GWU5
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

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A
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.91 Å
  • R-Value Free: 0.114 
  • R-Value Work: 0.103 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.390α = 90.00
b = 63.050β = 90.00
c = 69.170γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Data collection, Database references