Pseudobacteroides cellulosolvens pseudo-CphB

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


The structure of cyanophycinase in complex with a cyanophycin degradation intermediate.

Sharon, I.Grogg, M.Hilvert, D.Schmeing, T.M.

(2022) Biochim Biophys Acta Gen Subj 1866: 130217-130217

  • DOI: https://doi.org/10.1016/j.bbagen.2022.130217
  • Primary Citation of Related Structures:  
    7UQV, 7UQW

  • PubMed Abstract: 

    Cyanophycinases are serine protease family enzymes which are required for the metabolism of cyanophycin, the natural polymer multi-L-arginyl-poly(L-aspartic acid). Cyanophycinases degrade cyanophycin to β-Asp-Arg dipeptides, which enables use of this important store of fixed nitrogen. We used genetic code expansion to incorporate diaminopropionic acid into cyanophycinase in place of the active site serine, and determined a high-resolution structure of the covalent acyl-enzyme intermediate resulting from attack of cyanophycinase on a short cyanophycin segment. The structure indicates that cyanophycin dipeptide residues P1 and P1' bind shallow pockets adjacent to the catalytic residues. We observe many cyanophycinase - P1 dipeptide interactions in the co-complex structure. Calorimetry measurements show that at least two cyanophycin dipeptides are needed for high affinity binding to cyanophycinase. We also characterized a putative cyanophycinase which we found to be structurally very similar but that shows no activity and could not be activated by mutation of its active site. Despite its peptidic structure, cyanophycin is resistant to degradation by peptidases and other proteases. Our results help show how cyanophycinase can specifically bind and degrade this important polymer.

  • Organizational Affiliation

    Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C [auth D],
D [auth C]
275Pseudobacteroides cellulosolvens ATCC 35603 = DSM 2933Mutation(s): 0 
Gene Names: Bccel_3994
Find proteins for A0A0L6JSP1 (Pseudobacteroides cellulosolvens ATCC 35603 = DSM 2933)
Explore A0A0L6JSP1 
Go to UniProtKB:  A0A0L6JSP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0L6JSP1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.797α = 90
b = 172.797β = 90
c = 116.938γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
pointlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada178084

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description