3EN0

The Structure of Cyanophycinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structural basis of beta-peptide-specific cleavage by the serine protease cyanophycinase.

Law, A.M.Lai, S.W.Tavares, J.Kimber, M.S.

(2009) J.Mol.Biol. 392: 393-404

  • DOI: 10.1016/j.jmb.2009.07.001

  • PubMed Abstract: 
  • Cyanophycin, or poly-L-Asp-multi-L-Arg, is a non-ribosomally synthesized peptidic polymer that is used for nitrogen storage by cyanobacteria and other select eubacteria. Upon synthesis, it self-associates to form insoluble granules, the degradation o ...

    Cyanophycin, or poly-L-Asp-multi-L-Arg, is a non-ribosomally synthesized peptidic polymer that is used for nitrogen storage by cyanobacteria and other select eubacteria. Upon synthesis, it self-associates to form insoluble granules, the degradation of which is uniquely catalyzed by a carboxy-terminal-specific protease, cyanophycinase. We have determined the structure of cyanophycinase from the freshwater cyanobacterium Synechocystis sp. PCC6803 at 1.5-A resolution, showing that the structure is dimeric, with individual protomers resembling aspartyl dipeptidase. Kinetic characterization of the enzyme demonstrates that the enzyme displays Michaelis-Menten kinetics with a k(cat) of 16.5 s(-1) and a k(cat)/K(M) of 7.5x10(-6) M(-1) s(-1). Site-directed mutagenesis experiments confirm that cyanophycinase is a serine protease and that Gln101, Asp172, Gln173, Arg178, Arg180 and Arg183, which form a conserved pocket adjacent to the catalytic Ser132, are functionally critical residues. Modeling indicates that cyanophycinase binds the beta-Asp-Arg dipeptide residue immediately N-terminal to the scissile bond in an extended conformation in this pocket, primarily recognizing this penultimate beta-Asp-Arg residue of the polymeric chain. Because binding and catalysis depend on substrate features unique to beta-linked aspartyl peptides, cyanophycinase is able to act within the cytosol without non-specific cleavage events disrupting essential cellular processes.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyanophycinase
A, B, C
291Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: cphB
EC: 3.4.15.6
Find proteins for P73832 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P73832
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.156 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 75.847α = 90.00
b = 133.008β = 90.00
c = 164.306γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Source and taxonomy, Version format compliance