Structural basis for the allosteric control of the global transcription factor NtcA by the nitrogen starvation signal 2-oxoglutarate.
2-oxogluatarate (2-OG), a metabolite of the highly conserved Krebs cycle, not only plays a critical role in metabolism, but also constitutes a signaling molecule in a variety of organisms ranging from bacteria to plants and animals. In cyanobacteria, the accumulation of 2-OG constitutes the signal of nitrogen starvation and NtcA, a global transcription factor, has been proposed as a putative receptor for 2-OG. Here we present three crystal structures of NtcA from the cyanobacterium Anabaena: the apoform, and two ligand-bound forms in complex with either 2-OG or its analogue 2,2-difluoropentanedioic acid. All structures assemble as homodimers, with each subunit composed of an N-terminal effector-binding domain and a C-terminal DNA-binding domain connected by a long helix (C-helix). The 2-OG binds to the effector-binding domain at a pocket similar to that used by cAMP in catabolite activator protein, but with a different pattern. Comparative structural analysis reveals a putative signal transmission route upon 2-OG binding. A tighter coiled-coil conformation of the two C-helices induced by 2-OG is crucial to maintain the proper distance between the two F-helices for DNA recognition. Whereas catabolite activator protein adopts a transition from off-to-on state upon cAMP binding, our structural analysis explains well why NtcA can bind to DNA even in its apoform, and how 2-OG just enhances the DNA-binding activity of NtcA. These findings provided the structural insights into the function of a global transcription factor regulated by 2-OG, a metabolite standing at a crossroad between carbon and nitrogen metabolisms.
Zhao
Meng-Xi
MX
Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Jiang
Yong-Liang
YL
He
Yong-Xing
YX
Chen
Yi-Fei
YF
Teng
Yan-Bin
YB
Chen
Yuxing
Y
Zhang
Cheng-Cai
CC
Zhou
Cong-Zhao
CZ
D017033:Anabaena / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D000818:Animals; D000458:Cyanobacteria / Q000235:genetics / Q000378:metabolism; D002373:Cyclic AMP Receptor Protein / Q000235:genetics / Q000378:metabolism; D007656:Ketoglutaric Acids / Q000378:metabolism* / Q000494:pharmacology; D009584:Nitrogen / Q000378:metabolism*; D009603:Nitroso Compounds; D011485:Protein Binding / Q000235:genetics; D017433:Protein Structure, Secondary / Q000235:genetics; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics / Q000502:physiology; D053778:Thiazolidines; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
D002373:Cyclic AMP Receptor Protein; D007656:Ketoglutaric Acids; D009603:Nitroso Compounds; D053778:Thiazolidines; D014157:Transcription Factors; C040387:N-nitrosothiazolidine-4-carboxylic acid; D009584:Nitrogen