scholarly journals Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation–π bond

2019 ◽  
Vol 75 (6) ◽  
pp. 461-469 ◽  
Author(s):  
Jeffrey S. McFarlane ◽  
Trey A. Ronnebaum ◽  
Kathleen M. Meneely ◽  
Annemarie Chilton ◽  
Aron W. Fenton ◽  
...  
Keyword(s):  
Pyruvate Kinase ◽  
Functional Data ◽  
Human Liver ◽  
Phosphate Binding ◽  
Allosteric Site ◽  
Allosteric Activation ◽  
X Ray ◽  
Fructose 1,6 Bisphosphate ◽  
Open Position ◽  
Binding Loop

Human liver pyruvate kinase (hLPYK) converts phosphoenolpyruvate to pyruvate in the final step of glycolysis. hLPYK is allosterically activated by fructose-1,6-bisphosphate (Fru-1,6-BP). The allosteric site, as defined by previous structural studies, is located in domain C between the phosphate-binding loop (residues 444–449) and the allosteric loop (residues 527–533). In this study, the X-ray crystal structures of four hLPYK variants were solved to make structural correlations with existing functional data. The variants are D499N, W527H, Δ529/S531G (called GGG here) and S531E. The results revealed a conformational toggle between the open and closed positions of the allosteric loop. In the absence of Fru-1,6-BP the open position is stabilized, in part, by a cation–π bond between Trp527 and Arg538′ (from an adjacent monomer). In the S531E variant glutamate binds in place of the 6′-phosphate of Fru-1,6-BP in the allosteric site, leading to partial allosteric activation. Finally, the structure of the D499N mutant does not provide structural evidence for the previously observed allosteric activation of the D499N variant.

scholarly journals Structure, Function and Regulation of a Second Pyruvate Kinase Isozyme in Pseudomonas aeruginosa

2021 ◽  
Vol 12 ◽  
Author(s):  
Yassmin Abdelhamid ◽  
Meng Wang ◽  
Susannah L. Parkhill ◽  
Paul Brear ◽  
Xavier Chee ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Structure Function ◽  
Pyruvate Kinase ◽  
Amino Acid Sequence Identity ◽  
Conformational Transition ◽  
Allosteric Activation ◽  
X Ray ◽  
Directed Mutation ◽  
Sequence Identity ◽  
Allosteric Regulator

Pseudomonas aeruginosa (PA) depends on the Entner-Doudoroff pathway (EDP) for glycolysis. The main enzymatic regulator in the lower half of the EDP is pyruvate kinase. PA contains genes that encode two isoforms of pyruvate kinase, denoted PykAPA and PykFPA. In other well-characterized organisms containing two pyruvate kinase isoforms (such as Escherichia coli) each isozyme is differentially regulated. The structure, function and regulation of PykAPA has been previously characterized in detail, so in this work, we set out to assess the biochemical and structural properties of the PykFPA isozyme. We show that pykFPA expression is induced in the presence of the diureide, allantoin. In spite of their relatively low amino acid sequence identity, PykAPA and PykFPA display broadly comparable kinetic parameters, and are allosterically regulated by a very similar set of metabolites. However, the x-ray crystal structure of PykFPA revealed significant differences compared with PykAPA. Notably, although the main allosteric regulator binding-site of PykFPA was empty, the “ring loop” covering the site adopted a partially closed conformation. Site-directed mutation of the proline residues flanking the ring loop yielded apparent “locked on” and “locked off” allosteric activation phenotypes, depending on the residue mutated. Analysis of PykFPA inter-protomer interactions supports a model in which the conformational transition(s) accompanying allosteric activation involve re-orientation of the A and B domains of the enzyme and subsequent closure of the active site.

scholarly journals Analysis of progress curves. Interaction of pyruvate kinase from Escherichia coli with fructose 1,6-bisphosphate and calcium ions

1983 ◽  
Vol 211 (3) ◽  
pp. 631-640 ◽  
Author(s):  
A Boiteux ◽  
M Markus ◽  
T Plesser ◽  
B Hess ◽  
M Malcovati
Keyword(s):  
Escherichia Coli ◽  
Pyruvate Kinase ◽  
Allosteric Site ◽  
Binding Properties ◽  
Rate Analysis ◽  
Saturation Kinetics ◽  
Ph Stat ◽  
Stat Method ◽  
Fructose 1,6 Bisphosphate ◽  
Kinetics Of

The influence of fructose 1,6-bisphosphate and Ca2+ on the kinetics of pyruvate kinase from Escherichia coli K12 was studied (at pH 7.0 and 25 degrees C) by using the pH-stat method for the measurement of the reaction progress as well as initial-rate analysis. The data were analysed on the basis of a concerted model with three conformational states [Markus, Plesser, Boiteux, Hess & Malcovati (1980) Biochem. J. 189, 421-433] by using a novel procedure for a computer-directed treatment of progress curves [Markus & Plesser (1976) Biochem. Soc. Trans. 4, 361-364]. By addition of fructose 1,6-bisphosphate the sigmoid kinetics with respect to phosphoenolpyruvate and Mg2+ is abolished and the activity of the enzyme is described by classical saturation kinetics. This is explained by exclusive binding of fructose 1,6-bisphosphate at an allosteric site of the conformational state that forms the active complex. We observe that Ca2+ is an activator of the enzyme at low Mg2+ and Ca2+ concentrations; otherwise it is an inhibitor. These effects can be understood by assuming that Ca2+ has the same binding properties as Mg2+, although it does not allow a catalytic turnover.

Crystallization And Preliminary X-Ray Analysis Of Class Ii Fructose-1,6-Bisphosphate Aldolase From Thermus Caldophilus

2003 ◽  
Vol 10 (5) ◽  
pp. 511-515 ◽  
Author(s):  
Jun Lee ◽  
Young Im ◽  
Seong-Hwan Rho ◽  
Seong Park ◽  
Mun-Kyoung Kim ◽  
...  
Keyword(s):  
Class Ii ◽  
X Ray ◽  
Thermus Caldophilus ◽  
Fructose 1,6 Bisphosphate

scholarly journals Exploring the “minimal” structure of a functional ADAMTS13 by mutagenesis and small-angle X-ray scattering

Blood ◽  
2019 ◽  
Vol 133 (17) ◽  
pp. 1909-1918 ◽  
Author(s):  
Jian Zhu ◽  
Joshua Muia ◽  
Garima Gupta ◽  
Lisa A. Westfield ◽  
Karen Vanhoorelbeke ◽  
...  
Keyword(s):  
Small Angle ◽  
Columba Livia ◽  
Allosteric Activation ◽  
Complement Components ◽  
X Ray ◽  
X Ray Scattering ◽  
Morphogenetic Protein ◽  
Minimal Structure ◽  
Von Willebrand ◽  
Ray Scattering

Abstract Human ADAMTS13 is a multidomain protein with metalloprotease (M), disintegrin-like (D), thrombospondin-1 (T), Cys-rich (C), and spacer (S) domains, followed by 7 additional T domains and 2 CUB (complement components C1r and C1s, sea urchin protein Uegf, and bone morphogenetic protein-1) domains. ADAMTS13 inhibits the growth of von Willebrand factor (VWF)–platelet aggregates by cleaving the cryptic Tyr1605-Met1606 bond in the VWF A2 domain. ADAMTS13 is regulated by substrate-induced allosteric activation; without shear stress, the distal T8-CUB domains markedly inhibit VWF cleavage, and binding of VWF domain D4 or selected monoclonal antibodies (MAbs) to distal ADAMTS13 domains relieves this autoinhibition. By small angle X-ray scattering (SAXS), ADAMTS13 adopts a hairpin-like conformation with distal T7-CUB domains close to the proximal MDTCS domains and a hinge point between T4 and T5. The hairpin projects like a handle away from the core MDTCS and T7-CUB complex and contains distal T domains that are dispensable for allosteric regulation. Truncated constructs that lack the T8-CUB domains are not autoinhibited and cannot be activated by VWF D4 but retain the hairpin fold. Allosteric activation by VWF D4 requires T7, T8, and the 58–amino acid residue linker between T8 and CUB1. Deletion of T3 to T6 produced the smallest construct (delT3-6) examined that could be activated by MAbs and VWF D4. Columba livia (pigeon) ADAMTS13 (pADAMTS13) resembles human delT3-6, retains normal activation by VWF D4, and has a SAXS envelope consistent with amputation of the hairpin containing the dispensable T domains of human ADAMTS13. Our findings suggest that human delT3-6 and pADAMTS13 approach a “minimal” structure for allosterically regulated ADAMTS13.

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