Transition state analysis of adenosine nucleosidase from yellow lupin (Lupinus luteus)

Bates, Carl; Kendrick, Zachariah; McDonald, Nancy; Kline, Paul C.

doi:10.1016/j.phytochem.2005.10.006

Cited by 13 publications

(19 citation statements)

References 53 publications

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“…A sufficient set of KIEs and BIEs at the positions involved with bond motions can afford electrostatic and geometric constraints, when combined with computational modeling, to define an enzymatic TS (10-12). This information provides not only the atomic resolution of the transient structure at the highest energy summit along the reaction path, but also structural guidance for designing tight-binding TS analog inhibitors (13,14).Multiple approaches have been documented to measure KIEs and BIEs of enzymatic reactions (3,(15)(16)(17). A conventional method is to determine individual steady-state kinetic parameters (k cat and K m ) with a pair of isotopic substrates and then calculate their ratios (18).…”

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confidence: 99%

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Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8

Linscott

Kapilashrami

Wang

et al. 2016

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

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Protein lysine methyltransferases (PKMTs) catalyze the methylation of protein substrates, and their dysregulation has been linked to many diseases, including cancer. Accumulated evidence suggests that the reaction path of PKMT-catalyzed methylation consists of the formation of a cofactor(cosubstrate)-PKMT-substrate complex, lysine deprotonation through dynamic water channels, and a nucleophilic substitution (S N 2) transition state for transmethylation. However, the molecular characters of the proposed process remain to be elucidated experimentally. Here we developed a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method and corresponding mathematic matrix to determine precisely the ratios of isotopically methylated peptides. This approach may be generally applicable for examining the kinetic isotope effects (KIEs) of posttranslational modifying enzymes. Protein lysine methyltransferase SET8 is the sole PKMT to monomethylate histone 4 lysine 20 (H4K20) and its function has been implicated in normal cell cycle progression and cancer metastasis. We therefore implemented the MSbased method to measure KIEs and binding isotope effects (BIEs) of the cofactor S-adenosyl-L-methionine (SAM) for SET8-catalyzed H4K20 monomethylation. A primary intrinsic 13 C KIE of 1.04, an inverse intrinsic α-secondary CD 3 KIE of 0.90, and a small but statistically significant inverse CD 3 BIE of 0.96, in combination with computational modeling, revealed that SET8-catalyzed methylation proceeds through an early, asymmetrical S N 2 transition state with the C-N and C-S distances of 2.35-2.40 Å and 2.00-2.05 Å, respectively. This transition state is further supported by the KIEs, BIEs, and steadystate kinetics with the SAM analog Se-adenosyl-L-selenomethionine (SeAM) as a cofactor surrogate. The distinct transition states between protein methyltransferases present the opportunity to design selective transition-state analog inhibitors.S tepwise progression of an enzyme-catalyzed chemical reaction is accompanied by changes of bond orders and vibrational modes involved with specific atoms of the reactant(s) (1, 2). Such changes can be traced experimentally by measuring the ratios of turnover rates [kinetic isotope effects (KIEs)] or binding affinities [binding isotope effects (BIEs)] of the reactant(s) when the relevant atoms are replaced by heavy isotopes (3, 4). KIEs and BIEs are thus useful parameters for elucidating transition-state (TS) structures and catalytic mechanisms, which sometimes cannot be elucidated readily through sole measurement of steady-state kinetics (5-9). A sufficient set of KIEs and BIEs at the positions involved with bond motions can afford electrostatic and geometric constraints, when combined with computational modeling, to define an enzymatic TS (10-12). This information provides not only the atomic resolution of the transient structure at the highest energy summit along the reaction path, but also structural guidance for designing tight-binding TS analog inhibitors (13...

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mentioning

confidence: 99%

“…Multiple approaches have been documented to measure KIEs and BIEs of enzymatic reactions (3,(15)(16)(17). A conventional method is to determine individual steady-state kinetic parameters (k cat and K m ) with a pair of isotopic substrates and then calculate their ratios (18).…”

mentioning

confidence: 99%

Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8

Linscott

Kapilashrami

Wang

et al. 2016

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

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“…The purine bases can become a source of nitrogen under starvation conditions in plants and thus play an additional, essential role in their physiology. Adenosine-specific and non-specific NH enzymes have been characterized from yellow lupin [ 54 ] and Alaska pea seeds [ 55 ], respectively. Several putative NH genes have been annotated based on the presence of the amino-terminal NH-fingerprint sequence, and the products of the NH1 and NH2 genes from Arabidopsis thaliana have also shown activity toward the common nucleosides, including inosine, adenosine, and xanthosine, which can become a nitrogen source [ 56 ].…”

Section: Reviewmentioning

confidence: 99%

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases

Degano

2022

IJMS

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Enzymes catalyzing the hydrolysis of the N-glycosidic bond in nucleosides and other ribosides (N-ribohydrolases, NHs) with diverse substrate specificities are found in all kingdoms of life. While the overall NH fold is highly conserved, limited substitutions and insertions can account for differences in substrate selection, catalytic efficiency, and distinct structural features. The NH structural module is also employed in monomeric proteins devoid of enzymatic activity with different physiological roles. The homo-oligomeric quaternary structure of active NHs parallels the different catalytic strategies used by each isozyme, while providing a buttressing effect to maintain the active site geometry and allow the conformational changes required for catalysis. The unique features of the NH catalytic strategy and structure make these proteins attractive targets for diverse therapeutic goals in different diseases.

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“…The biotransformation pathways of the purine nucleosides, including adenosine 218, guanosine 219a and inosine 219b, by adenosine and guanosine-inosine nucleosidase isolated from yellow lupin (Lupinus luteus) have been investigated. 108,109 N6-Substituted purine derivatives, such as 216c, are natural cytokinins which play a unique role in the control of developmental processes in plants, and several different methods for extraction and purification of these cytokinins have been compared. 110 Adenosine has been identified as one of the major bioactive components in the traditional Chinese medicine 'qingkailing' (an injection).…”

Section: From Plantsmentioning

confidence: 99%

Muscarine, imidazole, oxazole and thiazole alkaloids

Jin

2009

Nat. Prod. Rep.

235

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Nature abounds with a great number of natural products containing five-membered heterocyclic subunits, such as imidazoles, oxazoles and thiazoles, and their corresponding saturated imidazolines, oxazolines and thiazolines. These naturally occurring metabolites often exhibit pharmacologically important biological activities. In this review, the isolation, biological activities, chemical synthetic studies, and biosynthetic pathways of these natural products are summarized.

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Transition state analysis of adenosine nucleosidase from yellow lupin (Lupinus luteus)

Cited by 13 publications

References 53 publications

Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8

Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases

Muscarine, imidazole, oxazole and thiazole alkaloids

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