Structure of the monopotassium salt of adenosine 5'-diphosphate dihydrate, KADP.2H<sub>2</sub>O

Adamiak, Dorota A.

doi:10.1107/s056774088000948x

Cited by 30 publications

(12 citation statements)

References 8 publications

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“…An anti conformation is preferred and most frequently reported for nucleoside 5 0 -diphosphate structures, e.g. ADP (Adamiak & Saenger, 1980;Shakked et al, 1980) and UDP (Viswamitra et al, 1979), and also in 2 0 :3 0isopropylideneadenosine (Sprang et al, 1978) and other nucleotides where the pyrophosphate structural motif can be found, e.g. NAD + (Reddy et al, 1981;Guillot et al, 2000).…”

Section: Geometry and Conformation Of The Nucleotide Moiety In (I) Anmentioning

confidence: 96%

“…not coordinated). The remaining three crystal structures are ADP potassium salt dihydrate [KADPHD01 (Adamiak & Saenger, 1980; H-atom positions not determined) and KADPHD02 (Swaminathan & Sundaralingam, 1980)], ADP rubidium salt monohydrate [RBADPM10 (Viswamitra et al, 1976); no H-atom positions] and ADP tris salt [tris is tris(hydroxymethyl)methylammonium] dihydrate [HMADPH (Shakked et al, 1980); no Hatom positions]. In KADPHD02, the positions of the H atoms seem to be incorrect; thus, an analysis of the hydrogen bonds in the K, Rb and tris salts of ADP is difficult.…”

Section: Comparison Of the Solid-state Conformation Of Ahdp With Adpmentioning

confidence: 99%

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Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine–hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts

et al. 2018

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Adenosine diphosphate (ADP) plays a crucial role in cell biochemistry, especially in metabolic pathways and energy storage. ADP itself, as well as many of its analogues, such as adenosine hypodiphosphate (AhDP), has been studied extensively, in particular in terms of enzymatic activity. However, structural studies in the solid state, especially for AhDP, are still missing. An analogue of ADP, i.e. adenosine hypodiphosphate ester, has been synthesized and characterized in the crystalline form as two hydrated sodium salts of 2':3'-isopropylideneadenosine 5'-hypodiphosphate (HAhDP, CHNOP for the neutral form), namely pentasodium tetrakis(2':3'-isopropylideneadenosine 5'-hypodiphosphate) tetracosahydrate, 5Na·3CHNOP·CHNOP·24HO or Na(HAhDP)(HAhDP)·24HO, (I), and sodium tetrakis(2':3'-isopropylideneadenosine 5'-hypodiphosphate) pentadecahydrate, Na·CHNOP·2CHNOP·CHNOP·15HO or Na(HAhDP)(HAhDP)(HAhDP)·15HO, (II). Crystal structure analyses of (I) and (II) reveal two nucleoside hypodiphosphate ions in the asymmetric units with different ionization states of the hypodiphosphate unit and adenine base. For all AhDP nucleotides, the same anti conformation about the N-glycosidic bond and similar puckering of the ribose ring have been found. AhDP geometry and interactions have been compared to ADP nucleotides deposited in the Cambridge Structural Database. The adenine-hypodiphosphate interactions, identified as defining nucleotide self-assembly, have been analysed in model systems, i.e. the adenine (Ade) salts of hypodiphosphoric acid, namely bis(adeninium) hypodiphosphate dihydrate, 2CHN·HPO·2HO or (AdeH)(HPO)·2HO, (III), and bis(adeninium) hypodiphosphate, 2CHN·HPO or (AdeH)(HPO), (IV).

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Section: Geometry and Conformation Of The Nucleotide Moiety In (I) Anmentioning

confidence: 96%

Section: Comparison Of the Solid-state Conformation Of Ahdp With Adpmentioning

confidence: 99%

Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine–hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts

et al. 2018

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“…Oligonucleotides were synthesized using nucleoside phosphoramidite derivatives obtained from Milligen (New Bedford, MA) and an Applied Biosystems 381A DNA synthesizer. High-performance liquid chromatography (HPLC) was carried out on an ODS-Hypersil column (0.46 × 25 cm, Shandon Southern, England), using a Beckman HPLC system. Absorption spectra were recorded by a Perkin-Elmer Lambda 3B UV/vis spectrophotometer.…”

Section: Methodsmentioning

confidence: 99%

Importance of Specific Adenosine N³-Nitrogens for Efficient Cleavage by a Hammerhead Ribozyme

1996

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Five modified hammerhead ribozyme/substrate complexes have been prepared in which individual adenosine N3-nitrogens have been excised and replaced with carbon. The modified complexes were chemically synthesized with the substitution of a single 3-deazzaadenosine (c3A) base analogue for residues A6, A9, A13, A14, or A15.1. Steady-state kinetic analyses indicate that the cleavage efficiencies, as measured by kcat/K(M), for the c3A6, c3A9, and c3A14 complexes were only marginally reduced (< or = 5-fold) relative to the native complex. By comparison, the cleavage efficiencies for the c3A13 and c315.1 complexes were reduced by 9-fold and 55-fold, respectively. these reductions in cleavage efficiency are primarily a result of lower kcat values. Profiles of pH and cleavage rate suggest that the chemical cleavage step is the rate-limiting reaction for these complexes. These results suggest that the N3-nitrogen of the A13 residue and particularly the A15.1 residue in the hammerhead ribozyme/substrate complex are critical for transition state stabilization and efficient cleavage activity. We have additionally compared the locations of these critical functional groups, as well as those identified from other studies, with recent crystallographic analyses. In some cases, the critical functional groups are clustered around proposed metal binding sites and may reflect functional groups critical for binding the metal cofactor. In other cases, clusters of functional groups may form a network of hydrogen bonds necessary for transition state stabilization.

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“…Note: We thank one of the referees for drawing our attention to a recent preliminary communication on the same structure . We have also learned from Dr W. Saenger, after this paper was submitted for publication, that he too had submitted a paper on the same crystal structure (Adamiak & Saenger, 1980) (previous paper). The overall features of the structure are the same in the two determinations with the exception of some significant differences in the geometrical parameters.…”

Section: Comparison Of the Molecular Conformations Of Adp And A Tp Inmentioning

confidence: 95%

The structure, chirality and zwitterionic character of potassium adenosine diphosphate dihydrate, KADP.2H₂O

Swaminathan¹,

Sundaralingam²

1980

Acta Crystallogr B Struct Sci

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IntroductionPotassium adenosine diphosphate dihydrate, K +.C10 HNNSOIOP~-. 2H20 , crystallizes in the orthorhombic space group P2~2~2 with four molecules in a unit cell of dimensions a --28.491 (6), b --10.446 (3) and c = 6.316 (1) A. The structure was solved by direct methods and refined to an R index of 0.062 (R w = 0.076) on 1384 intensities. The mean e.s.d.'s in bond lengths and angles are 0.013 A and 0.7 ° respectively. The crystal structure has revealed that the adenosine diphosphate exists as a zwitterion with N(1) of the base protonated and the pyrophosphate group dinegatively charged (one negative charge on each phosphate) and has provided details of the molecular conformation and chirality of the chelate ring. The two water molecules in the asymmetric unit are distributed over three positions, two on the same diad axis and one in a general position. The molecule is folded into one of the preferred compact conformations, viz. sugar pucker 2E (P---163.3 °, r m = 38.3°), the exocyclic C(4')-C(5') bond torsion angle ~ gauche + (57.8 °) and the glycosyl torsion angle X anti (32.4°), with an anionic oxygen of the o-phosphate and the hydroxyl oxygen of the fl-phosphate ligated to the K + ion. A second anionic oxygen of the fl-phosphate forms a slightly weaker coordination to the metal; thus, the metal ion is engaged in an tt,fl, fl chelate complex. In addition, the metal ion is coordinated to the base N(3), the ribose 0(2'), the anionic phosphate oxygen O(13) of neighboring nucleotides, and to one of the water molecules on the diad axis. Thus, the K + ion is surrounded by seven possible ligands. The chirality of the chelate ring corresponds to the A diastereomer. The N(1) and N(6) sites and N(6) and N(7) sites of the adenine base form pairs of hydrogen bonds with the oxygens of the ~-phosphate groups of neighboring molecules. There are no basestacking interactions observed in the structure.

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Structure of the monopotassium salt of adenosine 5'-diphosphate dihydrate, KADP.2H₂O

Cited by 30 publications

References 8 publications

Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine–hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts

Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine–hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts

Importance of Specific Adenosine N³-Nitrogens for Efficient Cleavage by a Hammerhead Ribozyme

The structure, chirality and zwitterionic character of potassium adenosine diphosphate dihydrate, KADP.2H₂O

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Structure of the monopotassium salt of adenosine 5'-diphosphate dihydrate, KADP.2H2O

Cited by 30 publications

References 8 publications

Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine–hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts

Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine–hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts

Importance of Specific Adenosine N3-Nitrogens for Efficient Cleavage by a Hammerhead Ribozyme

The structure, chirality and zwitterionic character of potassium adenosine diphosphate dihydrate, KADP.2H2O

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Product

Resources

About

Structure of the monopotassium salt of adenosine 5'-diphosphate dihydrate, KADP.2H₂O

Importance of Specific Adenosine N³-Nitrogens for Efficient Cleavage by a Hammerhead Ribozyme

The structure, chirality and zwitterionic character of potassium adenosine diphosphate dihydrate, KADP.2H₂O