Structural Studies of Metal Ions in Family II Pyrophosphatases:  The Requirement for a Janus Ion<sup>,</sup>

Fabrichniy, Igor P.; Lehtiö, L.; Salminen, Anu; Zyryanov, Anton B.; Baykov, Alexander A.; Lahti, Reijo; Goldman, Adrian

doi:10.1021/bi0484973

Cited by 33 publications

(77 citation statements)

References 27 publications

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“…The free Mg 2ϩ concentration was maintained at 20 mM. (His 98 ) interacts with the bound sulfate oxygen corresponding to the bridging oxygen of PP i (6,7,37). In contrast, none of the family I PPases whose structures have been previously resolved have His residues in their active sites.…”

Section: Discussionmentioning

confidence: 99%

An Unusual, His-dependent Family I Pyrophosphatase from Mycobacterium tuberculosis

Tammenkoski

Benini

Magretova

et al. 2005

Journal of Biological Chemistry

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Soluble inorganic pyrophosphatases (PPases) comprise two evolutionarily unrelated families (I and II). These two families have different specificities for metal cofactors, which is thought to be because of the fact that family II PPases have three active site histidines, whereas family I PPases have none. Here, we report the structural and functional characterization of a unique family I PPase from Mycobacterium tuberculosis (mtPPase) that has two His residues (His 21 and His 86 ) in the active site. The 1.3-Å three-dimensional structure of mtPPase shows that His 86 directly interacts with bound sulfate, which mimics the product phosphate. Otherwise, mtPPase is structurally very similar to the well studied family I hexameric PPase from Escherichia coli, although mtPPase lacks the intersubunit metal binding site found in E. coli PPase. The cofactor specificity of mtPPase resembles that of E. coli PPase in that it has high activity in the presence of Mg 2؉ , but it differs from the E. coli enzyme and family II PPases because it has much lower activity in the presence of Mn 2؉ or Zn 2؉ . Replacements of His 21 and His 86 in mtPPase with the residues found in the corresponding positions of E. coli PPase had either no effect on the Mg 2؉ -and Mn 2؉ -supported reactions (H86K) or reduced Mg 2؉ -supported activity (H21K). However, both replacements markedly increased the Zn 2؉ -supported activity of mtPPase (up to 11-fold). In the double mutant, Zn 2؉ was a 2.5-fold better cofactor than Mg 2؉ . These results show that the His residues in mtPPase are not essential for catalysis, although they determine cofactor specificity. Soluble inorganic pyrophosphatase (PPase)3 (EC 3.6.1.1), is an essential metal-dependent enzyme that converts pyrophosphate into orthophosphate. This simple reaction provides a thermodynamic pull for many biosynthetic reactions that yield pyrophosphate as a byproduct (1). Soluble PPases belong to two nonhomologous families (2, 3): family I PPases, which are fairly widespread in all types of organisms, and family II PPases, which are exclusive to bacteria. In eubacteria and archaebacteria, the family I PPases are usually homohexamers, whereas in eukaryotes, they are homodimers. In contrast, all family II PPases are homodimers. The subunit size is generally 19 -22 kDa in hexameric PPases and 31-34 kDa in dimeric forms. Despite the variability of the subunit size in family I PPases, their active site cavities are formed by the same 13 functionally important polar residues, which is reflected in the conservation of the catalytic mechanism (4, 5). Although no sequence or overall structural similarity is observed between the two families, there is a striking similarity in the spatial arrangement of six key active site residues, a remarkable example of convergent enzyme evolution (6, 7).Functionally, family II differs from family I in its preference for Mn 2ϩ over Mg 2ϩ as a cofactor. Mg 2ϩ is a better cofactor for family I PPases, and it also activates family II PPases to the same extent. However, Mn 2ϩ co...

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Section: Discussionmentioning

confidence: 99%

An Unusual, His-dependent Family I Pyrophosphatase from Mycobacterium tuberculosis

Tammenkoski

Benini

Magretova

et al. 2005

Journal of Biological Chemistry

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“…However, these enzymes also contain their own characteristic motifs further downstream ( Figure 3) and there is no evidence for any aspartylphosphate intermediate being formed. 52,59,60 In the PIN/5′-3′ nuclease domains, a catalytic Mg 2+ is chelated by the acidic residues including those occurring at the end of the S1 equivalent and the strand immediately to its left 51 activates a water for nucleophilic attack. In the TOPRIM domains of primases and topoisomerases the acidic residue at the end of the first strand is always a glutamate ( Figure 3) that acts as a general acid or base in the hydrolysis of the phosphoester bond or polynucleotide transfer.…”

Section: Relationship Of the Had Superfamily To Other Rossmannoid Foldsmentioning

confidence: 99%

Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes

Burroughs¹,

Allen²,

Dunaway‐Mariano³

et al. 2006

Journal of Molecular Biology

376

520

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The HAD (haloacid dehalogenase) superfamily includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates. The availability of numerous crystal structures of representatives belonging to diverse branches of the HAD superfamily provides us with a unique opportunity to reconstruct their evolutionary history and uncover the principal determinants that led to their diversification of structure and function. To this end we present a comprehensive analysis of the HAD superfamily that identifies their unique structural features and provides a detailed classification of the entire superfamily. We show that at the highest level the HAD superfamily is unified with several other superfamilies, namely the DHH, receiver (CheY-like), von Willebrand A, TOPRIM, classical histone deacetylases and PIN/FLAP nuclease domains, all of which contain a specific form of the Rossmannoid fold. These Rossmannoid folds are distinguished from others by the presence of equivalently placed acidic catalytic residues, including one at the end of the first core β-strand of the central sheet. The HAD domain is distinguished from these related Rossmannoid folds by two key structural signatures, a "squiggle" (a single helical turn) and a "flap" (a beta hairpin motif) located immediately downstream of the first β-strand of their core Rossmanoid fold. The squiggle and the flap motifs are predicted to provide the necessary mobility to these enzymes for them to alternate between the "open" and "closed" conformations. In addition, most members of the HAD superfamily contains inserts, termed caps, occurring at either of two positions in the core Rossmannoid fold. We show that the cap modules have been independently inserted into these two stereotypic positions on multiple occasions in evolution and display extensive evolutionary diversification independent of the core catalytic domain. The first group of caps, the C1 caps, is directly inserted into the flap motif and regulates access of reactants to the active site. The second group, the C2 caps, forms a roof over the active site, and access to their internal cavities might be in part regulated by the movement of the flap. The diversification of the cap module was a major factor in the exploration of a vast substrate space in the course of the evolution of this superfamily. We show that the HAD superfamily contains 33 major families distributed across the three superkingdoms of life. Analysis of the phyletic patterns suggests that at least five distinct HAD proteins are traceable to the last universal common ancestor (LUCA) of all extant organisms. While these prototypes diverged prior to the emergence Abbreviations used: HAD, haloacid dehalogenase; PNKP, polynucleotide kinase phosphatase; KDO 8-P, deoxy-Dmannose-octulosonate 8-phosphate; CTD, carboxyl-terminal domain; PNKP, polynucleotide kinase phosphatase; LUCA, last universal common ancestor.E-mail address of the corresponding author: aravind@ncbi.nlm.nih.gov of the LUCA, t...

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“…Three lines of evidence indicate that this substitution reduces the affinity of M1 in scPPX. First, despite numerous attempts to ensure binding with metal using high metal concentrations (up to 5-10 mM), this site is vacant in all scPPX crystal structures (data not shown) but is occupied in PPase structures (23,28). Second, the M1 site is occupied in the N35H mutant, similar to PPase (15).…”

Section: Discussionmentioning

confidence: 96%

“…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%

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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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Structural Studies of Metal Ions in Family II Pyrophosphatases: The Requirement for a Janus Ion^,

Cited by 33 publications

References 27 publications

An Unusual, His-dependent Family I Pyrophosphatase from Mycobacterium tuberculosis

An Unusual, His-dependent Family I Pyrophosphatase from Mycobacterium tuberculosis

Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes

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

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Structural Studies of Metal Ions in Family II Pyrophosphatases: The Requirement for a Janus Ion,

Cited by 33 publications

References 27 publications

An Unusual, His-dependent Family I Pyrophosphatase from Mycobacterium tuberculosis

An Unusual, His-dependent Family I Pyrophosphatase from Mycobacterium tuberculosis

Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes

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

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Resources

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Structural Studies of Metal Ions in Family II Pyrophosphatases: The Requirement for a Janus Ion^,