5N3U

The structure of the complex of CpcE and CpcF of phycocyanin lyase from Nostoc sp. PCC7120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 

wwPDB Validation  3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures and enzymatic mechanisms of phycobiliprotein lyases CpcE/F and PecE/F.

Zhao, C.Hoppner, A.Xu, Q.Z.Gartner, W.Scheer, H.Zhou, M.Zhao, K.H.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 13170-13175

  • DOI: 10.1073/pnas.1715495114

  • PubMed Abstract: 
  • The light-harvesting phycobilisome in cyanobacteria and red algae requires the lyase-catalyzed chromophorylation of phycobiliproteins. There are three functionally distinct lyase families known. The heterodimeric E/F type is specific for attaching bi ...

    The light-harvesting phycobilisome in cyanobacteria and red algae requires the lyase-catalyzed chromophorylation of phycobiliproteins. There are three functionally distinct lyase families known. The heterodimeric E/F type is specific for attaching bilins covalently to α-subunits of phycocyanins and phycoerythrins. Unlike other lyases, the lyase also has chromophore-detaching activity. A subclass of the E/F-type lyases is, furthermore, capable of chemically modifying the chromophore. Although these enzymes were characterized >25 y ago, their structures remained unknown. We determined the crystal structure of the heterodimer of CpcE/F from Nostoc sp. PCC7120 at 1.89-Å resolution. Both subunits are twisted, crescent-shaped α-solenoid structures. CpcE has 15 and CpcF 10 helices. The inner (concave) layer of CpcE (helices h2, 4, 6, 8, 10, 12, and 14) and the outer (convex) layer of CpcF (h16, 18, 20, 22, and 24) form a cavity into which the phycocyanobilin chromophore can be modeled. This location of the chromophore is supported by mutations at the interface between the subunits and within the cavity. The structure of a structurally related, isomerizing lyase, PecE/F, that converts phycocyanobilin into phycoviolobilin, was modeled using the CpcE/F structure as template. A H87C88 motif critical for the isomerase activity of PecE/F is located at the loop between h20 and h21, supporting the proposal that the nucleophilic addition of Cys-88 to C10 of phycocyanobilin induces the isomerization of phycocyanobilin into phycoviolobilin. Also, the structure of NblB, involved in phycobilisome degradation could be modeled using CpcE as template. Combined with CpcF, NblB shows a low chromophore-detaching activity.


    Organizational Affiliation

    State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P.R. China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule Chains Sequence Length Organism Details
Phycocyanobilin lyase subunit alpha
A
276 Nostoc sp. (strain PCC 7120 / UTEX 2576) Gene Names: cpcE
EC: 4.-.-.-
Find proteins for P07125 (Nostoc sp. (strain PCC 7120 / UTEX 2576))
Go to UniProtKB:  P07125
Entity ID: 2
Molecule Chains Sequence Length Organism Details
Phycocyanobilin lyase subunit beta
B
208 Nostoc sp. (strain PCC 7120 / UTEX 2576) Gene Names: cpcF
EC: 4.-.-.-
Find proteins for P29985 (Nostoc sp. (strain PCC 7120 / UTEX 2576))
Go to UniProtKB:  P29985
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å) Angle (°)
a = 74.600 α = 90.00
b = 59.825 β = 99.08
c = 110.634 γ = 90.00
Software Package:
Software Name Purpose
XDS data scaling
XDS data reduction
PHASER phasing
REFMAC refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references
  • Version 1.2: 2017-12-20
    Type: Database references