From Proteopedia
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| - | == Human protein phosphatase 2C == | + | == NolR == |
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| - | <Structure load='2IQ1' size='350' frame='true' align='right' caption='Quartenary structure of human protein phosphatase PP2Cm with Mg(II) (PDB ID 4DA1)' scene='Insert optional scene name here' /> Protein Phosphatases 2C are essencial enzymes involved in the regulation of several signaling pathways of branched-chain α-ketoacid dehydrogenase complex (BCKDC) by phosphorylation/dephosphorylation. The PP2C Family are Mg<sup>2+</sup> and Mn<sup>2+</sup> dependent monomeric proteins with two characteristic structural domains: a catalytic domain N-terminal with six alpha-helices, and a C-terminal region with three alpha-helices. The multienzyme complex uses numerous copies of three enzymes as major building blocks E1, E2 and E3. A dihydrolipoyl transacylase (E2) forms the core of the complex with 24 copies in octahedral symmetry.
| + | The symbiosis between rhizobial microbes and legume plants is fundamental to sustainable agriculture and ecological nitrogen cycling. This partnership requires coordinated expression of multiple genes to establish nitrogen-fixing nodules, with **NolR serving as a global transcriptional regulator** controlling this critical developmental process across diverse *Rhizobium* species. |
| - | The human branched-chain α-ketoacid dehydrogenase complex ser/thr phosphatase, PP2Cm, (BDP) is attached to the E2 core through non-covalent bonds. PP2Cm is distinguished from other groups of phosphatases by its structural distinction, absolute requirement for divalent cation, the <scene name='32/32/Protein_pp2cm_with_mgii/7'>beta-sheet sandwich</scene> catalytic domain and shows Mn<sup>2+</sup>/Mg<sup>2+</sup> dependent phosphatase activity. PP2Cm structure has two central antiparallel beta sheets that are flanked by alpha helices and the <scene name='32/32/Protein_pp2cm_with_mgii/4'>active site</scene> is located at one end of the beta-sheet sandwich containing two <scene name='32/32/Protein_pp2cm_with_mgii/6'>magnesium ions</scene> coordenated by <scene name='32/32/Protein_pp2cm_with_mgii/5'>Asp-109, Asp-208, Asp-298, and Asp-337</scene> residues.
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| - | At high levels of branched-chain ketoacids PP2Cm dephosphorylates Ser-337 and activates mitochondrial BCKDC complex by associating with the E2 component of the complex.
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| - | The water molecules at the binuclear metal centre coordinate the phosphate group of the substrate, each ion is hexa-coordinated by <scene name='32/32/Protein_pp2cm_with_mgii/8'>oxygen atoms</scene> from water, providing a nucleophile and general acid in the dephosphorylation reaction, and Arg33 creates a local positive electrostatic potential on the protein for recognition of the phosphate group of the substrate. The nucleophile is the metal-bridging water molecule which could attack the phosphorus atom in an S<sub>N</sub>2 mechanism. Coordination to two Mg<sup>2+</sup> ions may stabilize the morenucleophilic hydroxide ion species. Other ions such as Ca<sup>2+</sup>, Zn<sup>2+</sup> and Ni<sup>2+</sup> inactivate the enzyme by competitively inhibiting Mn<sup>2+</sup> or Mg<sup>2+</sup> binding.
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| - | == branched-chain α-ketoacid dehydrogenase complex ==
| + | We present the first high-resolution X-ray crystal structures of NolR in both unliganded and DNA-bound forms, revealing its complex interactions with asymmetric operator sequences. Analysis of NolR complexed with two different 22-base pair operator DNA sequences (oligos AT and AA) demonstrates that this **homodimeric transcription factor adopts a winged helix-turn-helix fold** and recognizes DNA through a combination of positively charged surface residues that engage the DNA phosphate backbone and specific base contacts. |
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| - | The human branched-chain α-ketoacid dehydrogenase (BCKD) complex is part of the mitochondrial α-ketoacid dehydrogenase complex family. Their structure consists of numerous copies of three enzymes E1, E2 and E3. A <scene name='32/32/E2b/1'> dihydrolipoyl transacylase (E2)</scene> forms the core | + | The most striking finding is a **conformational switching mechanism involving Gln56**, which alters its position to accommodate variation in target DNA sequences without changing overall binding affinity. This elegant mechanism allows NolR to regulate multiple nodulation and symbiosis genes with different operator sequences through modulation of thermodynamic binding contributions. The conformational flexibility of this key residue represents a novel regulatory strategy in the ArsR/SmtB transcription factor family. |
| - | of the complex with 24 copies in octahedral symmetry. Copies of the <scene name='32/32/E1/1'> α-ketoacid dehydrogenase (E1)</scene>, and copies of the<scene name='32/32/E3/2'> dihydrolipoamide dehydrogenase (E3)</scene>. In some types of (BCKDC) that are two regulatory enzymes proteins <scene name='32/32/Kinase/1'> protein kinase</scene> and <scene name='32/32/Phosphatase/1'> protein phosphatase</scene> that are attached to the E2 core through non-covalent bonds.
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| - | ==References, for further information on PP2Cm==
| + | These structural studies provide unprecedented molecular insight into **how NolR functions as a global regulatory hub**, proposing two distinct regulatory models for differential gene expression during nodule formation and symbiotic nitrogen fixation. This work illuminates the structural basis for one of nature's most important agricultural and ecological partnerships. |
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| - | * Ævarsson, A. ''et all'' "Crystal structure of human branched-chain α-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease", CellPress. [https://www.sciencedirect.com/science/article/pii/S0969212600001052].
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| - | * Wynn, R. M. ''et all'' "Structure, function and assembly of mammalian branched-chain α-ketoacid dehydrogenase complex", Alpha-Keto Acid Dehydrogenase Complexes. [https://link.springer.com/chapter/10.1007/978-3-0348-8981-0_7] | + | |
| - | * Lu, G. ''et all'' "Protein phosphatase 2Cm is a critical regulator of branched-chain amino acid catabolism in mice and cultured cells", The Journal of clinical investigation 119(6):1678-87. [https://www.researchgate.net/publication/24398300_Protein_phosphatase_2Cm_is_a_critical_regulator_of_branched-chain_amino_acid_catabolism_in_mice_and_cultured_cells]. | + | |
| - | * Pan, B. F ''et all'' "Regulation of PP2Cm expression by miRNA-204/211 and miRNA-22 in mouse and human cells [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816230/] | + | |
Revision as of 19:17, 10 November 2025
NolR
The symbiosis between rhizobial microbes and legume plants is fundamental to sustainable agriculture and ecological nitrogen cycling. This partnership requires coordinated expression of multiple genes to establish nitrogen-fixing nodules, with **NolR serving as a global transcriptional regulator** controlling this critical developmental process across diverse *Rhizobium* species.
We present the first high-resolution X-ray crystal structures of NolR in both unliganded and DNA-bound forms, revealing its complex interactions with asymmetric operator sequences. Analysis of NolR complexed with two different 22-base pair operator DNA sequences (oligos AT and AA) demonstrates that this **homodimeric transcription factor adopts a winged helix-turn-helix fold** and recognizes DNA through a combination of positively charged surface residues that engage the DNA phosphate backbone and specific base contacts.
The most striking finding is a **conformational switching mechanism involving Gln56**, which alters its position to accommodate variation in target DNA sequences without changing overall binding affinity. This elegant mechanism allows NolR to regulate multiple nodulation and symbiosis genes with different operator sequences through modulation of thermodynamic binding contributions. The conformational flexibility of this key residue represents a novel regulatory strategy in the ArsR/SmtB transcription factor family.
These structural studies provide unprecedented molecular insight into **how NolR functions as a global regulatory hub**, proposing two distinct regulatory models for differential gene expression during nodule formation and symbiotic nitrogen fixation. This work illuminates the structural basis for one of nature's most important agricultural and ecological partnerships.
