Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium

Moréra, Solange; Chiadmi, M.; Lebras, G.; Lascu, Ioan; Janin, Joël

doi:10.1021/bi00035a011

Cited by 123 publications

(118 citation statements)

References 48 publications

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“…One is the intermediary phosphorylation of enzymes [5][6][7][8][9][10], of which nucleoside diphosphate kinase is a particularly well-studied example. The other is the reversible protein histidine phosphorylation by protein kinases and phosphatases [3,11].…”

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confidence: 99%

Identification and characterization of a mammalian 14‐kDa phosphohistidine phosphatase

Pettersson

et al. 2002

European Journal of Biochemistry

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Protein histidine phosphorylation in eukaryotes has been sparsely studied compared to protein serine/threonine and tyrosine phosphorylation. In an attempt to rectify this by probing porcine liver cytosol with the phosphohistidinecontaining peptide succinyl-Ala-His(P)-Pro-Phe-p-nitroanilide (phosphopeptide I), we observed a phosphatase activity that was insensitive towards okadaic acid and EDTA. This suggested the existence of a phosphohistidine phosphatase different from protein phosphatase 1, 2A and 2C. A 1000-fold purification to apparent homogeneity gave a 14-kDa phosphatase with a specific activity of 3 lmolAEmin )1 AEmg )1 at pH 7.5 with 7 lM phosphopeptide I as substrate. Partial amino-acid sequence determination of the purified porcine enzyme by MS revealed similarity with a human sequence representing a human chromosome 9 gene of hitherto unknown function. Molecular cloning from a human embryonic kidney cell cDNAlibrary followed by expression and purification, yielded a protein with a molecular mass of 13 700 Da, and an EDTA-insensitive phosphohistidine phosphatase activity of 9 lmolAEmin )1 AEmg )1 towards phosphopeptide I. No detectable activity was obtained towards a set of phosphoserine-, phosphothreonine-, and phosphotyrosine peptides. Northern blot analysis indicated that the human phosphohistidine phosphatase mRNA was present preferentially in heart and skeletal muscle. These results provide a new tool for studying eukaryotic histidine phosphorylation/dephosphorylation.Keywords: dephosphorylation; N-phosphorylation; phosphoamidase; phosphopeptide; protein histidine phosphatase.Boyer and coworkers detected protein-bound phosphohistidine in rat-liver mitochondrial succinyl-CoA synthetase almost 40 years ago [1,2]. Despite the long time interval and the fact that phosphohistidine represents a substantial fraction of eukaryotic protein-bound phosphate [3], only a few phosphohistidine-containing proteins have been detected compared to the large number of eukaryotic proteins phosphorylated on serine, threonine and tyrosine residues. One reason for this difference may be that the N-bound phosphate of phosphohistidine easily escapes detection by common analytical procedures, due to its lability under acidic conditions, e.g. during fixation and staining of gels after SDS/PAGE [4].The studies on eukaryotic protein histidine phosphorylation and dephosphorylation have dealt with essentially two aspects. One is the intermediary phosphorylation of enzymes [5][6][7][8][9][10], of which nucleoside diphosphate kinase is a particularly well-studied example. The other is the reversible protein histidine phosphorylation by protein kinases and phosphatases [3,11]. An important contribution to the latter field was the purification of a yeast protein histidine kinase in 1991 [12]. Access to this enzyme also made possible the preparation of 32 P-labelled histone H4, which was later used as substrate in the search for phosphohistidine phosphatases. Using such an approach, the catalytic subunits of the well-studied serine/...

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confidence: 99%

Identification and characterization of a mammalian 14‐kDa phosphohistidine phosphatase

Pettersson

et al. 2002

European Journal of Biochemistry

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“…The reaction was started by addition of 10 l of substrate solution containing 12 mM [ 14 C]NaHCO 3 , 0.3 mM EDTA, 0.1 M Mops pH 7, and 1.5 mM DAPA; 5-l aliquots were quenched in 10% acetic acid at defined times and taken to dryness on a hotplate to remove unreacted [ 14 C]CO 2 . The residue was dissolved with a small volume of water, and 14 C radioactivity was detected by scintillation counting. As a control, crystals were left for 2 h in 30 l of the buffer solution, and the supernatant was assayed for catalytic activity.…”

Section: Methodsmentioning

confidence: 99%

“…In these cases [alkaline phosphatase (12), fructose-2,6-bisphosphatase (13), and nucleoside diphosphate kinase (14)], a histidine side chain is phosphorylated during the catalytic reaction. Here, we report the structure of the complex of DTBS with the mixed carbamic phosphoric acid anhydride intermediate, the first crystal structure of a substrate-derived phosphorylated reaction intermediate trapped during the catalytic reaction.…”

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Snapshot of a phosphorylated substrate intermediate by kinetic crystallography

Käck

Gibson

Lindqvist

et al. 1998

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

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The ATP-dependent enzyme dethiobiotin synthetase from Escherichia coli catalyses the formation of dethiobiotin from CO 2 and 7,8-diaminopelargonic acid. The reaction is initiated by the formation of a carbamate and proceeds through a phosphorylated intermediate, a mixed carbamic phosphoric anhydride. Here, we report the crystal structures at 1.9-and 1.6-Å resolution, respectively, of the enzyme-MgATP-diaminopelargonic acid and enzymeMgADP-carbamic-phosphoric acid anhydride complexes, observed by using kinetic crystallography. Reaction initiation by addition of either NaHCO 3 or diaminopelargonic acid to crystals already containing cosubstrates resulted in the accumulation of the phosphorylated intermediate at the active site. The phosphoryl transfer step shows inversion of the configuration at the phosphorus atom, consistent with an in-line attack by the carbamate oxygen onto the phosphorus atom of ATP. A key feature in the structure of the complex of the enzyme with the reaction intermediate is two magnesium ions, bridging the phosphates at the cleavage site. These magnesium ions compensate the negative charges at both phosphate groups after phosphoryl transfer and contribute to the stabilization of the reaction intermediate.A catalytic strategy used by many enzymes is to use nucleotide triphosphates, in particular ATP, for leaving group activation. In general, this strategy can be accomplished by transfer of the ␥-phosphoryl group of the nucleotide to the substrate. The resulting phosphorylated intermediate decomposes into phosphate and product. The penultimate enzyme in the biotin biosynthetic pathway, dethiobiotin synthetase (DTBS), uses this strategy. This enzyme catalyzes the ATP-dependent formation of the cyclic urea dethiobiotin from (7R,8S)-diaminononanoic acid [7,8-diaminopelargonic acid (DAPA)] and CO 2 . As a catalyst, the enzyme is rather inefficient, with k cat ϭ 1.5 min Ϫ1 under standard assay conditions (2, 4). DTBS was first studied by Eisenberg (1, 2), who proposed that the reaction consists of several steps (Fig. 1). The first step, formation of a DAPA carbamate, later was shown to proceed regiospecifically at N7 (3-5). The second proposed intermediate, a mixed carbamic-phosphoric acid anhydride formed by transfer of the ␥-phosphoryl group of ATP to a carbamate oxygen (6), has been isolated, with a lifetime of Ϸ25 min under certain conditions (7). It has been suggested that the last step, ring closure, proceeds through a tetrahedral intermediate (3).The three-dimensional structure of the enzyme (5, 8, 9) revealed a homodimer with the two equivalent active sites, separated by Ϸ25 Å, at the interface between the two subunits. The structure of DTBS is similar to the structure of other phosphotransferases, in particular adenylate kinase (10) and p21ras (11). Crystallographic studies (3) of complexes of DTBS with DAPA and͞or a nonhydrolyzable ATP analogue, adenylyl [␤,␥-methylene]diphosphonate (AMPPCP), suggested that conformational changes during catalysis were minor and that these crysta...

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“…[11][12][13][14] The family of NDPKs consists of two groups. The first group includes four members, NDPK-A, NDPK-B, NDPK-C, and NDPK-D, also known as NME1, NME2, NME3, and NME4, respectively, which are ubiquitously expressed.…”

Section: Regulation Of G-protein Signaling By Ndpks Backgroundmentioning

confidence: 99%

Regulation of heterotrimeric G-protein signaling by NDPK/NME proteins and caveolins: an update

Abu-Taha

Heijman

Feng

et al. 2018

Laboratory Investigation

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Heterotrimeric G proteins are pivotal mediators of cellular signal transduction in eukaryotic cells and abnormal G-protein signaling plays an important role in numerous diseases. During the last two decades it has become evident that the activation status of heterotrimeric G proteins is both highly localized and strongly regulated by a number of factors, including a receptor-independent activation pathway of heterotrimeric G proteins that does not involve the classical GDP/GTP exchange and relies on nucleoside diphosphate kinases (NDPKs). NDPKs are NTP/NDP transphosphorylases encoded by the nme/nm23 genes that are involved in a variety of cellular events such as proliferation, migration, and apoptosis. They therefore contribute, for example, to tumor metastasis, angiogenesis, retinopathy, and heart failure. Interestingly, NDPKs are translocated and/or upregulated in human heart failure. Here we describe recent advances in the current understanding of NDPK functions and how they have an impact on local regulation of G-protein signaling.

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Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium

Cited by 123 publications

References 48 publications

Identification and characterization of a mammalian 14‐kDa phosphohistidine phosphatase

Identification and characterization of a mammalian 14‐kDa phosphohistidine phosphatase

Snapshot of a phosphorylated substrate intermediate by kinetic crystallography

Regulation of heterotrimeric G-protein signaling by NDPK/NME proteins and caveolins: an update

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