5XN6

Heterodimer crystal structure of geranylgeranyl diphosphate synthases 1 with GGPPS Recruiting Protein(OsGRP) from Oryza sativa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A recruiting protein of geranylgeranyl diphosphate synthase controls metabolic flux toward chlorophyll biosynthesis in rice

Zhou, F.Wang, C.Y.Gutensohn, M.Jiang, L.Zhang, P.Zhang, D.Dudareva, N.Lu, S.

(2017) Proc Natl Acad Sci U S A 114: 6866-6871

  • DOI: https://doi.org/10.1073/pnas.1705689114
  • Primary Citation of Related Structures:  
    5XN5, 5XN6

  • PubMed Abstract: 

    In plants, geranylgeranyl diphosphate (GGPP) is produced by plastidic GGPP synthase (GGPPS) and serves as a precursor for vital metabolic branches, including chlorophyll, carotenoid, and gibberellin biosynthesis. However, molecular mechanisms regulating GGPP allocation among these biosynthetic pathways localized in the same subcellular compartment are largely unknown. We found that rice contains only one functionally active GGPPS, OsGGPPS1, in chloroplasts. A functionally active homodimeric enzyme composed of two OsGGPPS1 subunits is located in the stroma. In thylakoid membranes, however, the GGPPS activity resides in a heterodimeric enzyme composed of one OsGGPPS1 subunit and GGPPS recruiting protein (OsGRP). OsGRP is structurally most similar to members of the geranyl diphosphate synthase small subunit type II subfamily. In contrast to members of this subfamily, OsGRP enhances OsGGPPS1 catalytic efficiency and specificity of GGPP production on interaction with OsGGPPS1. Structural biology and protein interaction analyses demonstrate that affinity between OsGRP and OsGGPPS1 is stronger than between two OsGGPPS1 molecules in homodimers. OsGRP determines OsGGPPS1 suborganellar localization and directs it to a large protein complex in thylakoid membranes, consisting of geranylgeranyl reductase (OsGGR), light-harvesting-like protein 3 (OsLIL3), protochlorophyllide oxidoreductase (OsPORB), and chlorophyll synthase (OsCHLG). Taken together, genetic and biochemical analyses suggest OsGRP functions in recruiting OsGGPPS1 from the stroma toward thylakoid membranes, thus providing a mechanism to control GGPP flux toward chlorophyll biosynthesis.


  • Organizational Affiliation

    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Os07g0580900 proteinA,
C [auth B],
E
305Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os07g0580900OJ1301_C12.3OSNPB_070580900P0453G03.27
UniProt
Find proteins for Q7XI92 (Oryza sativa subsp. japonica)
Explore Q7XI92 
Go to UniProtKB:  Q7XI92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7XI92
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Os02g0668100 proteinB [auth C],
D,
F
304Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os02g0668100OJ1725_H08.13OSNPB_020668100
UniProt
Find proteins for Q6ET88 (Oryza sativa subsp. japonica)
Explore Q6ET88 
Go to UniProtKB:  Q6ET88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ET88
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.062α = 109.39
b = 102.981β = 109.59
c = 103.486γ = 109.13
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
HKL-2000data reduction
HKL-2000data reduction
HKL-2000data reduction
HKLdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of science and technology of the people's republic of ChinaChina#2013CB127004

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2018-09-19
    Changes: Data collection
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description