9I09 | pdb_00009i09

The Paulinella chromatophore transit peptide part2 (crTPpart2) of RnaH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

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Ligand Structure Quality Assessment 


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Literature

The Paulinella chromatophore transit peptide part2 adopts a structural fold similar to the gamma-glutamyl-cyclotransferase fold.

Klimenko, V.Reiners, J.Applegate, V.Reimann, K.Popowicz, G.Hoeppner, A.Papadopoulos, A.Smits, S.H.J.Nowack, E.C.M.

(2025) Plant Physiol 199

  • DOI: https://doi.org/10.1093/plphys/kiaf504
  • Primary Citation of Related Structures:  
    9I08, 9I09

  • PubMed Abstract: 

    The chromatophores of the cercozoan amoeba Paulinella are photosynthetic organelles that evolved from a cyanobacterial endosymbiont. Many nucleus-encoded chromatophore-targeted proteins carry unusual N-terminal targeting signals termed crTPs, which are bipartite. crTPpart1 likely mediates trafficking through the secretory pathway and is cleaved off during import, but crTPpart2 remains attached to its cargo protein and its function is unknown. To unravel the functional role of crTPpart2, here we elucidated the structures of crTPpart2 from two different chromatophore-targeted proteins by X-ray crystallography at ∼2.3 Å resolution. Interestingly, the crTPpart2 of both proteins adopts a structural fold. Both structures share a conserved structured core and a flexible N-terminal arm. The structured core resembles proteins of the γ-glutamyl cyclotransferase superfamily within which crTPpart2 structures form a protein (sub)-family. The proposed catalytic center typical for proteins with cyclotransferase activity is not conserved in crTPpart2. A Cys pair that is conserved in crTPpart2 of many chromatophore-targeted proteins has been captured as a disulfide bridge. Together, our data suggest that chromatophore-targeted proteins are imported in their folded state and that the fold adopted by crTPpart2 plays a functional role during import. The characterization of its structure and flexibility provides important steps toward elucidating this protein translocation mechanism.


  • Organizational Affiliation
    • Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transit peptide part2 (crTPpart2)318Paulinella chromatophoraMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.164α = 90
b = 81.164β = 90
c = 63.678γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoXDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany417919780
German Research Foundation (DFG)Germany267205415

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release