The Reaction Mechanism of Phospholipase D from Streptomyces sp. Strain PMF. Snapshots along the Reaction Pathway Reveal a Pentacoordinate Reaction Intermediate and an Unexpected Final Product

Leiros, Ingar; McSweeney, Seán; Hough, Edward

doi:10.1016/j.jmb.2004.04.003

Cited by 129 publications

(111 citation statements)

References 45 publications

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“…Vanadate readily accepts ligands to form a pentacovalent coordination complex with trigonal bipyramidal geometry (21). The x-ray structures of phosphotransferases complexed with vanadate provide a visual guide to the interactions that occur between active-site residues and the transition state(s) formed along the reaction coordinate that structures of phosphotransferases complexed with phosphate or phosphate ester substrates have, with only a few exceptions (10,(22)(23)(24), failed to do. To demonstrate the existence of a conserved trigonal bipyramidal mold in the HADSF phosphatase subfamily, a phosphate analog is needed that is more resistant to valency expansion than is vandate yet more pliable than orthophosphate (19,25).…”

Section: Resultsmentioning

confidence: 99%

The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state

Dunaway‐Mariano

Allen

2008

Proc. Natl. Acad. Sci. U.S.A.

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The evolution of new catalytic activities and specificities within an enzyme superfamily requires the exploration of sequence space for adaptation to a new substrate with retention of those elements required to stabilize key intermediates/transition states. Here, we propose that core residues in the large enzyme family, the haloalkanoic acid dehalogenase enzyme superfamily (HADSF) form a ''mold'' in which the trigonal bipyramidal transition states formed during phosphoryl transfer are stabilized by electrostatic forces. The vanadate complex of the hexose phosphate phosphatase BT4131 from Bacteroides thetaiotaomicron VPI-5482 (HPP) determined at 1.00 Å resolution via X-ray crystallography assumes a trigonal bipyramidal coordination geometry with the nucleophilic Asp-8 and one oxygen ligand at the apical position. Remarkably, the tungstate in the complex determined to 1.03 Å resolution assumes the same coordination geometry. The contribution of the general acid/base residue Asp-10 in the stabilization of the trigonal bipyramidal species via hydrogen-bond formation with the apical oxygen atom is evidenced by the 1.52 Å structure of the D10A mutant bound to vanadate. This structure shows a collapse of the trigonal bipyramidal geometry with displacement of the water molecule formerly occupying the apical position. Furthermore, the 1.07 Å resolution structure of the D10A mutant complexed with tungstate shows the tungstate to be in a typical ''phosphate-like'' tetrahedral configuration. The analysis of 12 liganded HADSF structures deposited in the protein data bank (PDB) identified stringently conserved elements that stabilize the trigonal bipyramidal transition states by engaging in favorable electrostatic interactions with the axial and equatorial atoms of the transferring phosphoryl group.phosphatase ͉ phosphoryl transfer ͉ transition state stabilization ͉ trigonal bipyramidal phosphorane

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Section: Resultsmentioning

confidence: 99%

The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state

Dunaway‐Mariano

Allen

2008

Proc. Natl. Acad. Sci. U.S.A.

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“…Interestingly, the electrostatic potential surface of a canonical PLD enzyme from Streptomyces (Leiros et al 2004) reveals that the active site of that enzyme is located at the bottom of a narrow cavity, which is bordered with negative charges (Fig. 3E).…”

Section: Resultsmentioning

confidence: 99%

“…Subsequently, the dZuc sequence of the active site loops (residues 162-171 and 202-220) was threaded onto the corresponding residues from the Nuc structure and their conformations were optimized using CNS 1.1 to avoid clashing and unfavorable configuration. (Leiros et al 2004) showing electrostatic surface potential (blue, positive; red, negative). The product phospholipid is shown in balland-stick representation highlighting the location of the enzyme active site.…”

Section: Modelingmentioning

confidence: 99%

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Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc

Voigt

Reuter

Kasaruho

et al. 2012

RNA

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Piwi-interacting RNAs (piRNAs) are a gonad-specific class of small RNAs that associate with the Piwi clade of Argonaute proteins and play a key role in transposon silencing in animals. Since biogenesis of piRNAs is independent of the doublestranded RNA-processing enzyme Dicer, an alternative nuclease that can process single-stranded RNA transcripts has been long sought. A Phospholipase D-like protein, Zucchini, that is essential for piRNA processing has been proposed to be a nuclease acting in piRNA biogenesis. Here we describe the crystal structure of Zucchini from Drosophila melanogaster and show that it is very similar to the bacterial endonuclease, Nuc. The structure also reveals that homodimerization induces major conformational changes assembling the active site. The active site is situated on the dimer interface at the bottom of a narrow groove that can likely accommodate single-stranded nucleic acid substrates. Furthermore, biophysical analysis identifies protein segments essential for dimerization and provides insights into regulation of Zucchini's activity.

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“…Phosphatidylserine is an important component of cell membrane phospholipids, which can regulate the functional status of key proteins in cell membrane, has important regulating effect on cellular metabolism, and acts as an in-termediate between cell membrane receptors and second receptors [20]. Phosphatidylserine synthase is a tool enzyme for synthesizing phosphatidylserine, belonging to the family of phosphatidyl diester synthase, which takes phospholipids as substrates, catalyzing transesterification between phospholipids and nucleophilic donors in the water [21]. Presently, functional phosphatidylserine synthase genes have been found in bacteria, yeast, mammals and plants.…”

Section: Discussionmentioning

confidence: 99%

Genetic analysis and fine mapping of an enclosed panicle mutant esp2 in rice (Oryza sativa L.)

et al. 2011

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The phenomenon of panicle enclosure in rice is mainly caused by the shortening of uppermost internode. Elucidating the molecular mechanism of panicle enclosure will be helpful for solving the problem of panicle enclosure in male sterile lines and creating new germplasms in rice. We acquired a monogenic recessive enclosed panicle mutant, named as esp2 (enclosed shorter panicle 2), from the tissue culture progeny of indica rice cultivar Minghui-86. In the mutant, panicles were entirely enclosed by flag leaf sheaths and the uppermost internode was almost completely degenerated, but the other internodes did not have obvious changes in length. Genetic analysis indicated that the mutant phenotype was controlled by a recessive gene, which could be steadily inherited and was not affected by genetic background. Apparently, ESP2 is a key gene for the development of uppermost internode in rice. Using an F 2 population of a cross between esp2 and a japonica rice cultivar Xiushui-13 as well as SSR and InDel markers, we fine mapped ESP2 to a 14-kb region on the end of the short arm of chromosome 1. According to the rice genome sequence annotation, only one intact gene exists in this region, namely, a putative phosphatidylserine synthase gene. Sequencing analysis on the mutant and the wild type indicated that this gene was inserted by a 5287-bp retrotransposon sequence. Hence, we took this gene as a candidate of ESP2. The results of this study will facilitate the cloning and functional analysis of ESP2 gene. rice, enclosed panicle mutant, ESP2 gene, fine mapping Citation:Guan H Z, Duan Y L, Liu H Q, et al. Genetic analysis and fine mapping of an enclosed panicle mutant esp2 in rice (Oryza sativa L.).

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The Reaction Mechanism of Phospholipase D from Streptomyces sp. Strain PMF. Snapshots along the Reaction Pathway Reveal a Pentacoordinate Reaction Intermediate and an Unexpected Final Product

Cited by 129 publications

References 45 publications

The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state

The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state

Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc

Genetic analysis and fine mapping of an enclosed panicle mutant esp2 in rice (Oryza sativa L.)

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