7LGJ

Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 8x(Asp-Arg)-NH2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures and function of the amino acid polymerase cyanophycin synthetase.

Sharon, I.Haque, A.S.Grogg, M.Lahiri, I.Seebach, D.Leschziner, A.E.Hilvert, D.Schmeing, T.M.

(2021) Nat Chem Biol 17: 1101-1110

  • DOI: https://doi.org/10.1038/s41589-021-00854-y
  • Primary Citation of Related Structures:  
    7LG5, 7LGJ, 7LGM, 7LGN, 7LGQ

  • PubMed Abstract: 

    Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-L-Asp residues with L-Arg residues attached to the β-carboxylate sidechains by isopeptide bonds. Cyanophycin is synthesized from ATP, aspartic acid and arginine by a homooligomeric enzyme called cyanophycin synthetase (CphA1). CphA1 has domains that are homologous to glutathione synthetases and muramyl ligases, but no other structural information has been available. Here, we present cryo-electron microscopy and X-ray crystallography structures of cyanophycin synthetases from three different bacteria, including cocomplex structures of CphA1 with ATP and cyanophycin polymer analogs at 2.6 Å resolution. These structures reveal two distinct tetrameric architectures, show the configuration of active sites and polymer-binding regions, indicate dynamic conformational changes and afford insight into catalytic mechanism. Accompanying biochemical interrogation of substrate binding sites, catalytic centers and oligomerization interfaces combine with the structures to provide a holistic understanding of cyanophycin biosynthesis.


  • Organizational Affiliation

    Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyanophycin synthase
A, B, C, D
879Synechocystis sp. PCC 6714Mutation(s): 0 
Gene Names: cphAD082_30240
EC: 6.3.2.29 (PDB Primary Data), 6.3.2.30 (PDB Primary Data)
UniProt
Find proteins for A0A068N621 (Synechocystis sp. (strain PCC 6714))
Explore A0A068N621 
Go to UniProtKB:  A0A068N621
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068N621
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
8x(Asp-Arg)-NH2
E, F, G, H
9synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
L [auth A]
M [auth A]
Q [auth B]
AA [auth D],
BA [auth D],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
V [auth C],
W [auth C]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
N [auth B]
O [auth B]
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
U [auth C],
X [auth D],
Y [auth D],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
7ID
Query on 7ID
E, F, G, H
L-PEPTIDE LINKINGC10 H19 N5 O5ASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2021-10-06
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Data collection, Derived calculations, Structure summary