8JBR | pdb_00008jbr

Structure of McyA2-CAPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.305 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.265 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history


Literature

Modular catalytic activity of nonribosomal peptide synthetases depends on the dynamic interaction between adenylation and condensation domains.

Peng, Y.J.Chen, Y.Zhou, C.Z.Miao, W.Jiang, Y.L.Zeng, X.Zhang, C.C.

(2024) Structure 32: 440

  • DOI: https://doi.org/10.1016/j.str.2024.01.010
  • Primary Citation of Related Structures:  
    8HLK, 8JBR

  • PubMed Abstract: 

    Nonribosomal peptide synthetases (NRPSs) are large multidomain enzymes for the synthesis of a variety of bioactive peptides in a modular and pipelined fashion. Here, we investigated how the condensation (C) domain and the adenylation (A) domain cooperate with each other for the efficient catalytic activity in microcystin NRPS modules. We solved two crystal structures of the microcystin NRPS modules, representing two different conformations in the NRPS catalytic cycle. Our data reveal that the dynamic interaction between the C and the A domains in these modules is mediated by the conserved "RXGR" motif, and this interaction is important for the adenylation activity. Furthermore, the "RXGR" motif-mediated dynamic interaction and its functional regulation are prevalent in different NRPSs modules possessing both the A and the C domains. This study provides new insights into the catalytic mechanism of NRPSs and their engineering strategy for synthetic peptides with different structures and properties.


  • Organizational Affiliation
    • Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
McyA protein1,041Microcystis aeruginosa PCC 7806Mutation(s): 0 
Gene Names: mcyA
UniProt
Find proteins for A8YJV7 (Microcystis aeruginosa (strain PCC 7806))
Explore A8YJV7 
Go to UniProtKB:  A8YJV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8YJV7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.305 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.265 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.99α = 90
b = 173.99β = 90
c = 78.033γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-01-24 
  • Deposition Author(s): Peng, Y.J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references
  • Version 1.2: 2024-07-03
    Changes: Database references