The “open” and “closed” structures of the type-C inorganic pyrophosphatases from Bacillus subtilis and Streptococcus gordonii

Ahn, Shinbyoung; Milner, Andrew; Fütterer, Klaus; Konopka, Monika; Ilias, Mohammad; Young, Tom; White, Scott A.

doi:10.1006/jmbi.2001.5070

Cited by 88 publications

(190 citation statements)

References 56 publications

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“…The stabilizing effect of Co 2ϩ is consistent with data showing that "canonical" family II PPases contain one site that tightly binds transition metal ions (Co 2ϩ or Mn 2ϩ ) in addition to several more loosely binding sites with broader specificity that are apparently filled with Mg 2ϩ in vivo (5,29,30). All of these sites have a role in catalysis, but the tightly bound transition metal ion also has a structural role (7,8) as it does in many other metalloenzymes. The activities of CBS-PPases preincubated with 0.1 mM Co 2ϩ were somewhat higher than those incubated with Mn 2ϩ .…”

Section: Production Of Ppases-supporting

confidence: 83%

Cystathionine β-Synthase (CBS) Domains Confer Multiple Forms of Mg2+-dependent Cooperativity to Family II Pyrophosphatases

Salminen

Anashkin

Lahti

et al. 2014

Journal of Biological Chemistry

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Section: Production Of Ppases-supporting

confidence: 83%

Cystathionine β-Synthase (CBS) Domains Confer Multiple Forms of Mg2+-dependent Cooperativity to Family II Pyrophosphatases

Salminen

Anashkin

Lahti

et al. 2014

Journal of Biological Chemistry

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“…StoneHingeD defines each hinge as a fixed point between connected regions undergoing large-scale opening and closing modes in DomDecomp. 12 Such pivot-like hinges are known for proteins including adenylate kinase, 13 inorganic pyrophosphatase, 14 and ribose binding protein. 15 To account for backbone flexibility during ligand docking, programs such as FlexDock have been developed to sample hinge rotations.…”

Section: Introductionmentioning

confidence: 99%

StoneHinge: Hinge prediction by network analysis of individual protein structures

et al. 2009

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Hinge motions are important for molecular recognition, and knowledge of their location can guide the sampling of protein conformations for docking. Predicting domains and intervening hinges is also important for identifying structurally self-determinate units and anticipating the influence of mutations on protein flexibility and stability. Here we present StoneHinge, a novel approach for predicting hinges between domains using input from two complementary analyses of noncovalent bond networks: StoneHingeP, which identifies domain-hinge-domain signatures in ProFlex constraint counting results, and StoneHingeD, which does the same for DomDecomp Gaussian network analyses. Predictions for the two methods are compared to hinges defined in the literature and by visual inspection of interpolated motions between conformations in a series of proteins. For StoneHingeP, all the predicted hinges agree with hinge sites reported in the literature or observed visually, although some predictions include extra residues. Furthermore, no hinges are predicted in six hinge-free proteins. On the other hand, StoneHingeD tends to overpredict the number of hinges, while accurately pinpointing hinge locations. By determining the consensus of their results, StoneHinge improves the specificity, predicting 11 of 13 hinges found both visually and in the literature for nine different open protein structures, and making no false-positive predictions. By comparison, a popular hinge detection method that requires knowledge of both the open and closed conformations finds 10 of the 13 known hinges, while predicting four additional, false hinges.

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“…In the absence of substrate, one more metal binding site containing two Asp and one His residues as ligands (M1 site) is observed in PPase (23,24,28). The Asp residues (39 and 127) are retained in scPPX, but His is replaced with Asn 35 .…”

Section: Discussionmentioning

confidence: 99%

“…The overall structure of yeast cytosolic PPX (scPPX) bears a striking similarity to that of the well characterized family II pyrophosphatase (PPase) (23,24), a DHH phosphoesterase that catalyzes a similar reaction with pyrophosphate, the shortest polyphosphate. Despite only 12-17% sequence identity, 11 of the total 14 polar residues in the active site of family II PPase are conserved in all yeast-type PPXs, and two more are conserved in most of the enzymes (Fig.…”

Section: Hismentioning

confidence: 99%

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Kinetic and Mutational Analyses of the Major Cytosolic Exopolyphosphatase from Saccharomyces cerevisiae

Tammenkoski

Moiseev

Lahti

et al. 2007

Journal of Biological Chemistry

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Yeast exopolyphosphatase (scPPX) processively splits off the terminal phosphate group from linear polyphosphates longer than pyrophosphate. scPPX belongs to the DHH phosphoesterase superfamily and is evolutionarily close to the well characterized family II pyrophosphatase (PPase -bound enzyme. These results provide an initial step toward understanding the dynamics of scPPX catalysis and reveal significant functional differences between structurally similar scPPX and family II PPase. Linear inorganic polyphosphates (polyP)3 comprising chains of tens to hundreds of phosphate units are conserved in all cells, and thus are possible agents of evolution from prebiotic times (1, 2). In eukaryotes, they account for up to 20% of dry cell weight (1, 2). Recent evidence indicates that rather than simply being a store of phosphate and energy, polyP are required for bacterial responses to a variety of stress and stringency conditions, as well as for virulence of some pathogens (3-5). PolyP are additionally involved in blood clotting (6) and proliferation of mammary cancer cells (7).PolyP are synthesized by polyphosphate kinase, and hydrolyzed by exo-and endopolyphosphatases. Exopolyphosphatase (PPX) processively releases the terminal phosphate groups from polyP formed by Ն3 phosphate residues. Based on the primary structure, PPXs are classified into two types, whose prototypes are PPXs from yeast (Saccharomyces cerevisiae) cytosol and Escherichia coli. Yeast-type PPX, reported in fungi and protozoa, belongs to the superfamily of DHH phosphoesterases (named after the conserved Asp-His-His motif) (8), whereas E. coli-type PPX is present in Eubacteria and Archaea and belongs to a sugar kinase/actin/hsp-70 superfamily (9). Genes of both yeast-type PPXs (from S. cerevisiae and Leishmania major) and E. coli type PPXs (from E. coli, Aquifex aeolicus and Sulfolobus solfataricus) have been expressed in E. coli (10 -14), and the structures of S. cerevisiae (15), E. coli (16), 4 and A. aeolicus (E. coli type) (18) PPXs have been determined. The overall folds of the two PPX families are dissimilar. Specifically, the subunits comprise two domains in yeast-type PPX and four domains in E. coli-type PPX. However, in both families, the active site is located between the domains connected by a flexible linker. Interestingly, yeast and A. aeolicus PPXs are monomeric proteins (15, 18 -20), whereas E. coli PPX is dimeric (10, 16). 4 Interestingly, the yeast cell contains up to five different exopolyphosphatases in different compartments (22).The overall structure of yeast cytosolic PPX (scPPX) bears a striking similarity to that of the well characterized family II pyrophosphatase (PPase) (23, 24), a DHH phosphoesterase that catalyzes a similar reaction with pyrophosphate, the shortest polyphosphate. Despite only 12-17% sequence identity, 11 of the total 14 polar residues in the active site of family II PPase are conserved in all yeast-type PPXs, and two more are conserved in most of the enzymes (Fig. 1A), implying an evolutionary relationship. M...

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The “open” and “closed” structures of the type-C inorganic pyrophosphatases from Bacillus subtilis and Streptococcus gordonii

Cited by 88 publications

References 56 publications

Cystathionine β-Synthase (CBS) Domains Confer Multiple Forms of Mg2+-dependent Cooperativity to Family II Pyrophosphatases

Cystathionine β-Synthase (CBS) Domains Confer Multiple Forms of Mg2+-dependent Cooperativity to Family II Pyrophosphatases

StoneHinge: Hinge prediction by network analysis of individual protein structures

Kinetic and Mutational Analyses of the Major Cytosolic Exopolyphosphatase from Saccharomyces cerevisiae

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