5Y2V

Strcutrue of the full-length CcmR complexed with 2-OG from Synechocystis PCC6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Coordinating carbon and nitrogen metabolic signaling through the cyanobacterial global repressor NdhR.

Jiang, Y.L.Wang, X.P.Sun, H.Han, S.J.Li, W.F.Cui, N.Lin, G.M.Zhang, J.Y.Cheng, W.Cao, D.D.Zhang, Z.Y.Zhang, C.C.Chen, Y.Zhou, C.Z.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 403-408

  • DOI: 10.1073/pnas.1716062115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The coordination of carbon and nitrogen metabolism is essential for bacteria to adapt to nutritional variations in the environment, but the underlying mechanism remains poorly understood. In autotrophic cyanobacteria, high CO <sub>2 </sub> levels fav ...

    The coordination of carbon and nitrogen metabolism is essential for bacteria to adapt to nutritional variations in the environment, but the underlying mechanism remains poorly understood. In autotrophic cyanobacteria, high CO 2 levels favor the carboxylase activity of ribulose 1,5 bisphosphate carboxylase/oxygenase (RuBisCO) to produce 3-phosphoglycerate, whereas low CO 2 levels promote the oxygenase activity of RuBisCO, leading to 2-phosphoglycolate (2-PG) production. Thus, the 2-PG level is reversely correlated with that of 2-oxoglutarate (2-OG), which accumulates under a high carbon/nitrogen ratio and acts as a nitrogen-starvation signal. The LysR-type transcriptional repressor NAD(P)H dehydrogenase regulator (NdhR) controls the expression of genes related to carbon metabolism. Based on genetic and biochemical studies, we report here that 2-PG is an inducer of NdhR, while 2-OG is a corepressor, as found previously. Furthermore, structural analyses indicate that binding of 2-OG at the interface between the two regulatory domains (RD) allows the NdhR tetramer to adopt a repressor conformation, whereas 2-PG binding to an intradomain cleft of each RD triggers drastic conformational changes leading to the dissociation of NdhR from its target DNA. We further confirmed the effect of 2-PG or 2-OG levels on the transcription of the NdhR regulon. Together with previous findings, we propose that NdhR can sense 2-OG from the Krebs cycle and 2-PG from photorespiration, two key metabolites that function together as indicators of intracellular carbon/nitrogen status, thus representing a fine sensor for the coordination of carbon and nitrogen metabolism in cyanobacteria.


    Organizational Affiliation

    Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China; zcz@ustc.edu.cn cczhang@ihb.ac.cn cyxing@ustc.edu.cn.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui, 230027, People's Republic of China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China zcz@ustc.edu.cn cczhang@ihb.ac.cn cyxing@ustc.edu.cn.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rubisco operon transcriptional regulator
A, B, C, D
324Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: rbcR
Find proteins for P73862 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P73862
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
B, D
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.766α = 90.00
b = 109.160β = 90.00
c = 178.226γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31630001, 31500598

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Database references