8K48 | pdb_00008k48

LTD of arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.245 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.220 (DCC) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

LTD coordinates chlorophyll biosynthesis and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN transport.

Rong, L.An, J.Chen, X.Wang, C.Wu, J.Wang, P.Zheng, Y.Wang, X.Chai, X.Li, W.Hu, Z.Lu, D.Chen, G.E.Ouyang, M.Grimm, B.Zhang, L.Xu, X.

(2025) Plant Cell 37

  • DOI: https://doi.org/10.1093/plcell/koaf068
  • Primary Citation of Related Structures:  
    8K48

  • PubMed Abstract: 

    Chlorophyll biosynthesis must be tightly coupled to light-harvesting chlorophyll a/b-binding protein (LHCP) biogenesis, as free chlorophyll and its precursors are phototoxic. However, precisely how these 2 processes are coordinated in Arabidopsis (Arabidopsis thaliana) remains elusive. Our previous studies demonstrated the role of LHCP TRANSLOCATION DEFECT (LTD) in delivering LHCPs to the chloroplast via the signal recognition particle-dependent pathway. Here, we show that LTD interacts with and stabilizes the chlorophyll biosynthesis enzymes Mg-protoporphyrin methyltransferase and Mg-protoporphyrin monomethylester (MgPME) cyclase, maintaining their activity. We also demonstrate the direct binding of LTD to MgPME, and through crystal structure analysis, we show that the groove of the LTD dimer is critical for MgPME binding. Thus, we propose that LTD transfers MgPME from Mg-protoporphyrin methyltransferase to the MgPME cyclase. These results elucidate a role for LTD in synchronizing chlorophyll biosynthesis with LHCP transport to ensure the correct insertion of chlorophylls into LHCPs.


  • Organizational Affiliation
    • The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Key Laboratory of Synthetic Biology and Biomanufacturing, School of Life Sciences, Henan University, Kaifeng 475004, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LHCP TRANSLOCATION DEFECT
A, B, C, D
113Arabidopsis thalianaMutation(s): 0 
Gene Names: LTDGDC1At1g50900F8A12.12
UniProt
Find proteins for Q8VY88 (Arabidopsis thaliana)
Explore Q8VY88 
Go to UniProtKB:  Q8VY88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VY88
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.220 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.776α = 90
b = 63.776β = 90
c = 225.397γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32170258

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references, Structure summary