Allosteric pyruvate kinase-based “logic gate” synergistically senses energy and sugar levels in Mycobacterium tuberculosis

Zhong, Weiguo; Liang, Cui; Goh, Boon Chong; Cai, Qixu; Ho, Peiying; Chionh, Yok Hian; Yuan, Meng; Sahili, Abbas El; Fothergill‐Gilmore, Linda A.; Walkinshaw, Malcolm D.; Lescar, Julien; Dedon, Peter C.

doi:10.1038/s41467-017-02086-y

Cited by 56 publications

(93 citation statements)

References 51 publications

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“…Recently, a binding site for G6P was identified in the crystal structures of Mtb PyK . This site, located at the interface of the A‐ and C‐domains near the canonical effector binding pocket, is formed by three helices Aα6, Cα1, Cα2, and the G6P‐loop at the N‐terminal end of Cα1.…”

Section: Architecture Of Pyksmentioning

confidence: 99%

“…Asn268's main chain nitrogen atom also forms a hydrogen bond with the sugar. Sequence of the G6P loop varies in PyKs of different organisms but is identical in different species of Mycobacterium . Remarkably, G6P and AMP exhibit synergistic allosteric activity .…”

Section: Architecture Of Pyksmentioning

confidence: 99%

“…In the Phe complex of PyK‐M2, a rigid body rotation of the A‐ and C‐domains forces Lys421 out of the binding pocket that is responsible for the stabilization of the active R‐state tetramer. AMP and G6P were found to synergistically activate Mtb PyK. A “rock‐shape‐lock” mechanism based on a concerted rocking motion has been proposed to explain the activation mechanism . In Mtb PyK AMP‐binding is accompanied by an interplay of two loops: the canonical effector loop (AMP‐loop) spanning residues 451–458, which remains flexible in the effector‐free state, and a C‐terminal tail loop comprising residues 467–472.…”

Section: Mechanisms Of Allosteric Regulationmentioning

confidence: 99%

“…In the last step of glycolysis, PyK (EC 2.7.1.40) catalyzes the irreversible transfer of phosphate from phosphoenolpyruvate (PEP) to ADP resulting in the production of PYR and ATP. PyK is a major regulator for controlling the metabolic flux and ATP production in glycolysis and is considered a potential drug target . However, because of the conserved architecture of the PyK active site and the central role of glycolysis in all organisms, developing selective inhibitors targeting the active site is challenging.…”

Section: Introductionmentioning

confidence: 99%

“…The main bottleneck in characterizing the mechanisms of allosteric regulation is the lack of structural data for many PyKs in the ligand‐free state and in complex with various ligands. Of the 97 crystal structures of PyKs deposited in the PDB, structures representing all four states of the protein (apo, substrate‐complex, effector‐complex, and substrate‐effector complex) are available only for PyKs of Leishmania mexicana ( Lm PyK), Mycobacterium tuberculosis ( Mtb PyK), and human PyK‐M2 (Table S1).…”

Section: Introductionmentioning

confidence: 99%

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An overview of structure, function, and regulation of pyruvate kinases

et al. 2019

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In the last step of glycolysis Pyruvate kinase catalyzes the irreversible conversion of ADP and phosphoenolpyruvate to ATP and pyruvic acid, both crucial for cellular metabolism. Thus pyruvate kinase plays a key role in controlling the metabolic flux and ATP production. The hallmark of the activity of different pyruvate kinases is their tight modulation by a variety of mechanisms including the use of a large number of physiological allosteric effectors in addition to their homotropic regulation by phosphoenolpyruvate. Binding of effectors signals precise and orchestrated movements in selected areas of the protein structure that alter the catalytic action of these evolutionarily conserved enzymes with remarkably conserved architecture and sequences. While the diverse nature of the allosteric effectors has been discussed in the literature, the structural basis of their regulatory effects is still not well understood because of the lack of data representing conformations in various activation states. Results of recent studies on pyruvate kinases of different families suggest that members of evolutionarily related families follow somewhat conserved allosteric strategies but evolutionarily distant members adopt different strategies. Here we review the structure and allosteric properties of pyruvate kinases of different families for which structural data are available.

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Section: Architecture Of Pyksmentioning

confidence: 99%

Section: Architecture Of Pyksmentioning

confidence: 99%

Section: Mechanisms Of Allosteric Regulationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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An overview of structure, function, and regulation of pyruvate kinases

et al. 2019

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Odd one out? Functional tuning of Zymomonas mobilis pyruvate kinase is narrower than its allosteric, human counterpart

et al. 2022

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Various protein properties are often illuminated using sequence comparisons of protein homologs. For example, in analyses of the pyruvate kinase multiple sequence alignment, the set of positions that changed during speciation ("phylogenetic" positions) were enriched for "rheostat" positions in human liver pyruvate kinase (hLPYK). (Rheostat positions are those which, when substituted with various amino acids, yield a range of functional outcomes).However, the correlation was moderate, which could result from multiple biophysical constraints acting on the same position during evolution and/or various sources of noise. To further examine this correlation, we here tested Zymomonas mobilis PYK (ZmPYK), which has <65% sequence identity to any other PYK sequence. Twenty-six ZmPYK positions were selected based on their phylogenetic scores, substituted with multiple amino acids, and assessed for changes in K app-PEP . Although we expected to identify multiple, strong rheostat positions, only one moderate rheostat position was detected. Instead, nearly half of the 271 ZmPYK variants were inactive and most others showed near wild-type function. Indeed, for the active ZmPYK variants, the total range of K app,PEP values ("tunability") was 40-fold less than that observed for hLPYK variants. The combined functional studies and sequence comparisons suggest that ZmPYK has evolved functional and/or structural attributes that differ from the rest of the family. We hypothesize that including such "orphan" sequences in MSA analyses obscures the correlations used to predict rheostat positions. Finally, results raise the intriguing biophysical question as to how the same protein fold can support rheostat positions in one homolog but not another.

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