scholarly journals Structural Analysis of the Bacterial HPr Kinase/Phosphorylase V267F Mutant Gives Insights into the Allosteric Regulation Mechanism of This Bifunctional Enzyme

2007 ◽  
Vol 282 (48) ◽  
pp. 34952-34957 ◽  
Author(s):  
Vincent Chaptal ◽  
Fanny Vincent ◽  
Virginie Gueguen-Chaignon ◽  
Vicente Monedero ◽  
Sandrine Poncet ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Allosteric Regulation ◽  
Regulation Mechanism ◽  
Bifunctional Enzyme

scholarly journals Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation

2020 ◽  
Vol 295 (51) ◽  
pp. 17425-17440
Author(s):  
Suparno Nandi ◽  
Mortezaali Razzaghi ◽  
Dhiraj Srivastava ◽  
Mishtu Dey
Keyword(s):  
Cancer Cells ◽  
Pyruvate Kinase ◽  
Allosteric Regulation ◽  
Glycolytic Enzyme ◽  
Structural Basis ◽  
Regulation Mechanism ◽  
Oligomeric State ◽  
Structural Reorganization ◽  
The Impact ◽  
Insight Into

Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme and transcriptional coactivator and is critical for tumor metabolism. In cancer cells, native tetrameric PKM2 is phosphorylated or acetylated, which initiates a switch to a dimeric/monomeric form that translocates into the nucleus, causing oncogene transcription. However, it is not known how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2. We explored this question via crystallographic and biophysical analyses of PKM2 mutants containing residues that mimic phosphorylation and acetylation. We find that the PTMs elicit major structural reorganization of the fructose 1,6-bisphosphate (FBP), an allosteric activator, binding site, impacting the interaction with FBP and causing a disruption in oligomerization. To gain insight into how these modifications might cause unique outcomes in cancer cells, we examined the impact of increasing the intracellular pH (pHi) from ∼7.1 (in normal cells) to ∼7.5 (in cancer cells). Biochemical studies of WT PKM2 (wtPKM2) and the two mimetic variants demonstrated that the activity decreases as the pH is increased from 7.0 to 8.0, and wtPKM2 is optimally active and amenable to FBP-mediated allosteric regulation at pHi 7.5. However, the PTM mimetics exist as a mixture of tetramer and dimer, indicating that physiologically dimeric fraction is important and might be necessary for the modified PKM2 to translocate into the nucleus. Thus, our findings provide insight into how PTMs and pH regulate PKM2 and offer a broader understanding of its intricate allosteric regulation mechanism by phosphorylation or acetylation.

scholarly journals An alternative allosteric regulation mechanism of an acidophilicl-lactate dehydrogenase fromEnterococcus mundtii15-1A

FEBS Open Bio ◽  
2014 ◽  
Vol 4 (1) ◽  
pp. 834-847 ◽  
Author(s):  
Yasuyuki Matoba ◽  
Masashi Miyasako ◽  
Koichi Matsuo ◽  
Kosuke Oda ◽  
Masafumi Noda ◽  
...  
Keyword(s):  
Lactate Dehydrogenase ◽  
Allosteric Regulation ◽  
Regulation Mechanism

scholarly journals Exploring the Allosteric Mechanism of Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase 2 (SHP2) by Molecular Dynamics Simulations

2020 ◽  
Vol 8 ◽  
Author(s):  
Quan Wang ◽  
Wen-Cheng Zhao ◽  
Xue-Qi Fu ◽  
Qing-Chuan Zheng
Keyword(s):  
Molecular Dynamics ◽  
Protein Tyrosine Phosphatase ◽  
Tyrosine Phosphatase ◽  
Allosteric Regulation ◽  
Sh2 Domain ◽  
Regulation Mechanism ◽  
Protein Tyrosine ◽  
Src Homology 2 ◽  
Activated State ◽  
Src Homology

The Src homology-2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP2, encoded by PTPN11) is a critical allosteric phosphatase for many signaling pathways. Programmed cell death 1 (PD-1) could be phosphorylated at its immunoreceptor tyrosine-based inhibitory motif (ITIM) and immunoreceptor tyrosine-based switch motif (ITSM) and can bind to SHP2 to initiate T cell inactivation. Although the interaction of SHP2-PD-1 plays an important role in the immune process, the complex structure and the allosteric regulation mechanism remain unknown. In this study, molecular dynamics (MD) simulations were performed to study the binding details of SHP2 and PD-1, and explore the allosteric regulation mechanism of SHP2. The results show that ITIM has a preference to bind to the N-SH2 domain and ITSM has almost the same binding affinity to the N-SH2 and C-SH2 domain. Only when ITIM binds to the N-SH2 domain and ITSM binds to the C-SH2 domain can the full activation of SHP2 be obtained. The binding of ITIM and ITSM could change the motion mode of SHP2 and switch it to the activated state.

scholarly journals Structural and mechanistic insights into the bifunctional enzyme isocitrate dehydrogenase kinase/phosphatase AceK

2012 ◽  
Vol 367 (1602) ◽  
pp. 2656-2668 ◽  
Author(s):  
Jimin Zheng ◽  
Susan P. Yates ◽  
Zongchao Jia
Keyword(s):  
Structural Analysis ◽  
Active Site ◽  
Isocitrate Dehydrogenase ◽  
Krebs Cycle ◽  
Evolutionary Relationship ◽  
Bifunctional Enzyme ◽  
Eukaryotic Protein Kinase ◽  
Glyoxylate Bypass ◽  
Regulatory Motifs

The switch between the Krebs cycle and the glyoxylate bypass is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK). AceK, a bifunctional enzyme, phosphorylates and dephosphorylates isocitrate dehydrogenase (IDH) with its unique active site that harbours both the kinase and ATP/ADP-dependent phosphatase activities. AceK was the first example of prokaryotic phosphorylation identified, and the recent characterization of the structures of AceK and its complex with its protein substrate, IDH, now offers a new understanding of both previous and future endeavours. AceK is structurally similar to the eukaryotic protein kinase superfamily, sharing many of the familiar catalytic and regulatory motifs, demonstrating a close evolutionary relationship. Although the active site is shared by both the kinase and phosphatase functions, the catalytic residues needed for phosphatase function are readily seen when compared with the DXDX(T/V) family of phosphatases, despite the fact that the phosphatase function of AceK is strictly ATP/ADP-dependent. Structural analysis has also allowed a detailed look at regulation and its stringent requirements for interacting with IDH.

The investigation of allosteric regulation mechanism of analgesic effect using SD rat taste bud tissue biosensor

2019 ◽  
Vol 126 ◽  
pp. 815-823 ◽  
Author(s):  
Sa Xiao ◽  
Yanqing Zhang ◽  
Panpan Song ◽  
Junbo Xie ◽  
Guangchang Pang
Keyword(s):  
Analgesic Effect ◽  
Allosteric Regulation ◽  
Taste Bud ◽  
Regulation Mechanism ◽  
Sd Rat

scholarly journals Allosteric Regulation Mechanism of Trimeric Membrane

2016 ◽  
Vol 110 (3) ◽  
pp. 383a
Author(s):  
Yuhang Wang ◽  
Abhi Singharoy ◽  
Klaus Schulten ◽  
Emad Tajkhorshid
Keyword(s):  
Allosteric Regulation ◽  
Regulation Mechanism

Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism*

2018 ◽  
Vol 475 (14) ◽  
pp. 2395-2416 ◽  
Author(s):  
Dirk Maurer ◽  
Bernhard Lohkamp ◽  
Michael Krumpel ◽  
Mikael Widersten ◽  
Doreen Dobritzsch
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Allosteric Regulation ◽  
Fruit Fly ◽  
Product Inhibition ◽  
Enzyme Activation ◽  
Site Directed Mutagenesis ◽  
Regulation Mechanism ◽  
Dependent Manner ◽  
Ph Dependent

β-Ureidopropionase (βUP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. Nitrilase-like βUPs use a tetrad of conserved residues (Cys233, Lys196, Glu119 and Glu207) for catalysis and occur in a variety of oligomeric states. Positive co-operativity toward the substrate N-carbamoyl-β-alanine and an oligomerization-dependent mechanism of substrate activation and product inhibition have been reported for the enzymes from some species but not others. Here, the activity of recombinant human βUP is shown to be similarly regulated by substrate and product, but in a pH-dependent manner. Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. Only at physiological pH is the enzyme responsive to effector binding, with N-carbamoyl-β-alanine causing association to more active higher molecular mass species, and β-alanine dissociation to inactive dimers. The parallel between the pH and ligand-induced effects suggests that protonation state changes play a crucial role in the allosteric regulation mechanism. Disruption of dimer–dimer interfaces by site-directed mutagenesis generated dimeric, inactive enzyme variants. The crystal structure of the T299C variant refined to 2.08 Å resolution revealed high structural conservation between human and fruit fly βUP, and supports the hypothesis that enzyme activation by oligomer assembly involves ordering of loop regions forming the entrance to the active site at the dimer–dimer interface, effectively positioning the catalytically important Glu207 in the active site.

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