1
|
An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis. Proc Natl Acad Sci U S A 2016; 113:13750-13755. [PMID: 27849620 DOI: 10.1073/pnas.1613610113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
HD domain phosphohydrolase enzymes are characterized by a conserved set of histidine and aspartate residues that coordinate an active site metallocenter. Despite the important roles these enzymes play in nucleotide metabolism and signal transduction, few have been both biochemically and structurally characterized. Here, we present X-ray crystal structures and biochemical characterization of the Bacillus megaterium HD domain phosphohydrolase OxsA, involved in the biosynthesis of the antitumor, antiviral, and antibacterial compound oxetanocin-A. These studies reveal a previously uncharacterized reaction for this family; OxsA catalyzes the conversion of a triphosphorylated compound into a nucleoside, releasing one molecule of inorganic phosphate at a time. Remarkably, this functionality is a result of the OxsA active site, which based on structural and kinetic analyses has been tailored to bind the small, four-membered ring of oxetanocin-A over larger substrates. Furthermore, our OxsA structures show an active site that switches from a dinuclear to a mononuclear metal center as phosphates are eliminated from substrate.
Collapse
|
2
|
Christmann M, Hu J, Kitamura M, Stoltz B. Tetrahedron reports on organic chemistry. Tetrahedron 2015. [DOI: 10.1016/s0040-4020(15)00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
3
|
Enzymatic synthesis of acyclic nucleoside thiophosphonate diphosphates: Effect of the α-phosphorus configuration on HIV-1 RT activity. Antiviral Res 2015; 117:122-31. [DOI: 10.1016/j.antiviral.2015.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 01/08/2023]
|
4
|
Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2013. [DOI: 10.1016/s0040-4020(13)01252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
5
|
Iranpoor N, Firouzabadi H, Khalili D. The First Mitsunobu Protocol for Efficient Synthesis of α-Acyloxyphosphonates Using 4,4′-Azopyridine. PHOSPHORUS SULFUR 2011. [DOI: 10.1080/10426507.2011.582594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Nasser Iranpoor
- a Department of Chemistry, College of Sciences , Shiraz University , Shiraz, Iran
| | - Habib Firouzabadi
- a Department of Chemistry, College of Sciences , Shiraz University , Shiraz, Iran
| | - Dariush Khalili
- a Department of Chemistry, College of Sciences , Shiraz University , Shiraz, Iran
| |
Collapse
|
6
|
Vorontsov II, Minasov G, Kiryukhina O, Brunzelle JS, Shuvalova L, Anderson WF. Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex. J Biol Chem 2011; 286:33158-66. [PMID: 21757692 PMCID: PMC3190883 DOI: 10.1074/jbc.m111.250456] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP pool in bacteria. Biochemical assays of the EF1143 dNTPase activity demonstrated nonspecific hydrolysis of all canonical dNTPs in the presence of Mn(2+). In contrast, with Mg(2+) hydrolysis required the presence of dGTP as an effector, activating the degradation of dATP and dCTP with dGTP also being consumed in the reaction with dATP. The crystal structure of EF1143 and dynamic light scattering measurements in solution revealed a tetrameric oligomer as the most probable biologically active unit. The tetramer contains four dGTP specific allosteric regulatory sites and four active sites. Examination of the active site with the dATP substrate suggests an in-line nucleophilic attack on the α-phosphate center as a possible mechanism of the hydrolysis and two highly conserved residues, His-129 and Glu-122, as an acid-base catalytic dyad. Structural differences between EF1143 apo and holo forms revealed mobility of the α3 helix that can regulate the size of the active site binding pocket and could be stabilized in the open conformation upon formation of the tetramer and dGTP effector binding.
Collapse
Affiliation(s)
- Ivan I Vorontsov
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | | | | |
Collapse
|
7
|
Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2011. [DOI: 10.1016/s0040-4020(11)00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Cai L, Ban L, Guan W, Mrksich M, Wang PG. Enzymatic synthesis and properties of uridine-5'-O-(2-thiodiphospho)-N-acetylglucosamine. Carbohydr Res 2011; 346:1576-80. [PMID: 21645883 DOI: 10.1016/j.carres.2011.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 05/03/2011] [Accepted: 05/05/2011] [Indexed: 12/19/2022]
Abstract
This paper describes an enzymatic approach to obtain a thio-containing UDP-GlcNAc analog. We use an assay based on capture of the carbohydrate and analysis by mass spectrometry to quantitatively characterize the activity of this unnatural sugar donor in a LgtA-mediated glycosylation reaction.
Collapse
Affiliation(s)
- Li Cai
- Departments of Chemistry and Biochemistry, The Ohio State University, 484 W. 12th Ave., Columbus, OH 43210, USA
| | | | | | | | | |
Collapse
|
9
|
Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2010. [DOI: 10.1016/s0040-4020(10)01735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
10
|
López-Cortina S, Medina-Arreguin A, Hernández-Fernández E, Bernès S, Guerrero-Alvarez J, Ordoñez M, Fernández-Zertuche M. Stereochemistry of base-induced cleavage of methoxide ion on cis- and trans-1,4-diphenylphosphorinanium salts. A different behavior with a phenyl substituent. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.05.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
11
|
Tetrahedron reports on organic chemistry. Tetrahedron 2008. [DOI: 10.1016/s0040-4020(08)00897-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
12
|
Zimmerman MD, Proudfoot M, Yakunin A, Minor W. Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli. J Mol Biol 2008; 378:215-26. [PMID: 18353368 DOI: 10.1016/j.jmb.2008.02.036] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 02/13/2008] [Accepted: 02/16/2008] [Indexed: 11/19/2022]
Abstract
HD-domain phosphohydrolases have nucleotidase and phosphodiesterase activities and play important roles in the metabolism of nucleotides and in signaling. We present three 2.1-A-resolution crystal structures (one in the free state and two complexed with natural substrates) of an HD-domain phosphohydrolase, the Escherichia coli 5'-nucleotidase YfbR. The free-state structure of YfbR contains a large cavity accommodating the metal-coordinating HD motif (H33, H68, D69, and D137) and other conserved residues (R18, E72, and D77). Alanine scanning mutagenesis confirms that these residues are important for activity. Two structures of the catalytically inactive mutant E72A complexed with Co(2+) and either thymidine-5'-monophosphate or 2'-deoxyriboadenosine-5'-monophosphate disclose the novel binding mode of deoxyribonucleotides in the active site. Residue R18 stabilizes the phosphate on the Co(2+), and residue D77 forms a strong hydrogen bond critical for binding the ribose. The indole side chain of W19 is located close to the 2'-carbon atom of the deoxyribose moiety and is proposed to act as the selectivity switch for deoxyribonucleotide, which is supported by comparison to YfdR, another 5'-nucleotidase in E. coli. The nucleotide bases of both deoxyriboadenosine-5'-monophosphate and thymidine-5'-monophosphate make no specific hydrogen bonds with the protein, explaining the lack of nucleotide base selectivity. The YfbR E72A substrate complex structures also suggest a plausible single-step nucleophilic substitution mechanism. This is the first proposed molecular mechanism for an HD-domain phosphohydrolase based directly on substrate-bound crystal structures.
Collapse
Affiliation(s)
- Matthew D Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA
| | | | | | | |
Collapse
|
13
|
Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)01371-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
14
|
Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)00834-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
15
|
Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)00205-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
16
|
|
17
|
Benner SA, Glasfeld A, Piccirilli JA. Stereospecificity in Enzymology: Its Place in Evolution. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9780470147283.ch3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
|
18
|
Cummins JH, Potter BVL. A General Chemical Method for the Stereochemical Analysis of Nucleoside-5′ [16o,18o] Phosphorothioates. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/03086648708079134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jane H. Cummins
- a Department of Chemistry , University of Leicester , Leicester , LE1 7RH , U. K
| | - Barry V. L. Potter
- a Department of Chemistry , University of Leicester , Leicester , LE1 7RH , U. K
| |
Collapse
|
19
|
Lectka T, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2006. [DOI: 10.1016/s0040-4020(06)01801-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
20
|
Frey PA. Chiral phosphorothioates: stereochemical analysis of enzymatic substitution at phosphorus. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 62:119-201. [PMID: 2658487 DOI: 10.1002/9780470123089.ch4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- P A Frey
- Institute for Enzyme Research, Graduate School, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53705
| |
Collapse
|
21
|
Gerlt JA, Coderre JA, Mehdi S. Oxygen chiral phosphate esters. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 55:291-380. [PMID: 6312782 DOI: 10.1002/9780470123010.ch4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
During the past four years, methods have been reported for the syntheses and configurational analyses of virtually any phosphate mono- and diester chiral by virtue of oxygen isotope substitution, and these techniques have already been applied to an impressive number of enzymic and chemical reactions. At present, no experimental information is available that contradicts the simplest interpretations that have been applied to the results obtained for enzymic reactions: inversion of configuration indicating a direct displacement of the leaving group by the attacking group, and retention of configuration implying the formation of a phosphorylated or nucleotidylated enzyme intermediate. However, it does seem necessary to further investigate the mechanisms of at least some of the reactions discussed in this review to ensure that the simplest interpretation is correct. For example, the caveat we have raised about the interpretation of inversions of configurations in phosphohydrolase reactions is chemically reasonable, and these reactions should be reexamined to evaluate the importance of covalent catalysis by carboxylate groups. However, for the vast majority of the enzymic reactions that have been investigated, the stereochemical approach to ascertaining whether catalysis involves the formation of covalent intermediates remains the simplest and most direct method.
Collapse
|
22
|
Lectka T, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2006. [DOI: 10.1016/s0040-4020(06)00771-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
23
|
López-Cortina S, Basiulis DI, Marsi KL, Muñoz-Hernández MA, Ordoñez M, Fernández-Zertuche M. Synthesis of new 1,3-oxaphosphorinanium salts. Stereochemistry of hydroxide-induced displacement of methoxide ion. J Org Chem 2006; 70:7473-8. [PMID: 16149773 DOI: 10.1021/jo050901w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] The synthesis of pure cis- and trans-3-methoxy-2,2,6-trimethyl-3-phenyl-1,3-oxaphosphorinanium tetrafluoroborate salts 3a and 3b, respectively, molecules designed to evaluate the effect of oxygen on the steric course of base-induced nucleophilic displacement of the methoxy group at phosphorus, was accomplished. It was found that these isomeric salts react with aqueous sodium hydroxide to produce the corresponding phosphine oxides 7a and 7b with complete retention of configuration at phosphorus.
Collapse
Affiliation(s)
- Susana López-Cortina
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | | | | | | | | | | |
Collapse
|
24
|
Eckstein F. Phosphorothioatanaloga von Nucleotiden - Werkzeuge zur Untersuchung biochemischer Prozesse. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.19830950603] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
25
|
Posner PG, Motherwell PW. Tetrahedron reports on organic chemistry. Tetrahedron 2004. [DOI: 10.1016/s0040-4020(04)01396-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
26
|
Pires de Castro CS, SouzaDe JR, Bloch C. Mechanism of DNA cleavage catalyzed by Mung Bean Nuclease. Inorganica Chim Acta 2004. [DOI: 10.1016/j.ica.2004.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
27
|
Tetrahedron reports on organic chemistry. Tetrahedron 2004. [DOI: 10.1016/s0040-4020(04)00315-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
28
|
Posner PG, Motherwell PW. Tetrahedron reports on organic chemistry. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)01884-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
29
|
Posner PG, Motherwell PW. Tetrahedron reports on organic chemistry. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)01130-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
Posner PG, Motherwell PW. Tetrahedron reports on organic chemistry. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00841-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
31
|
Tetrahedron reports on organic chemistry. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00323-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
32
|
Otvös L, Bajor Z, Kraicsovits F, Sági G, Tegyey Z. Synthesis and enzymatic characterization of P1-thio-P2-oxo trideoxynucleoside diphosphates having AZT, FdU, or dT at the 3'-position. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2003; 21:79-92. [PMID: 11991151 DOI: 10.1081/ncn-120006533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Model compounds for oligonucleotide-prodrugs, P1-thio-P2-oxo-trideoxyribonucleoside diphosphates: d[G(s)C(o)X] and d[T(s)A(o)X] (X = AZT, FdU or dT) have been prepared, and their hydrolyses by snake venom phosphodiesterase and nuclease S1 are described.
Collapse
Affiliation(s)
- László Otvös
- Chemical Research Center, Institute of Chemistry, Hungarian Academy of Sciences, Budapest
| | | | | | | | | |
Collapse
|
33
|
Posner G, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)01503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
34
|
Abstract
Inversion of configuration at phosphorus during ribozyme-catalyzed cleavage of RNA is usually considered unequivocal proof of in-line attack, but the relevant pseudorotation diagram for formation of the 2('),3(')-cyclic phosphate shows that inversion is not inconsistent with adjacent attack as long as breakdown of the trigonal bipyramid is in-line. For the reaction to occur by adjacent attack, a normally unstable apical oxyanion in the trigonal bipyramidal intermediate would have to be stabilized. Density-functional calculations show that a metal ion such as magnesium could perform this stabilization. We conclude that the possibility of adjacent attack should not be too hastily dismissed in cases where the setup is closer to adjacent than to in-line geometry.
Collapse
Affiliation(s)
- Ralf Stowasser
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | | |
Collapse
|
35
|
Mathew KM, Ravi S, Sontakke CV, Chander H. Synthesis of deoxyadenosine-5?-(35S)-thiomonophosphate [dAMP(35S)] of high specific activity - a key intermediate for the synthesis of Sp-deoxyadenosine-5?-(alpha;-35S)-thiotriphosphate [Sp-dATP (?-35S)]. J Labelled Comp Radiopharm 2002. [DOI: 10.1002/jlcr.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
36
|
Cullis PM, Fawcett J, Griffith GA, Harger MJ, Lee M. Mechanism and stereochemistry of diphosphate formation from dioxaphosphorinanes: a critical reassessment. J Am Chem Soc 2001; 123:4147-54. [PMID: 11457177 DOI: 10.1021/ja004084n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of diphosphate formation from (R)-2-chloro-2-oxo-5,5-dimethyl-4-(R)-phenyl-1,3,2-dioxaphosphorinane (5a) and 2-hydroxy-2-oxo-5,5-dimethyl-4-(R)-phenyl-1,3,2-dioxaphosphorinane (6) has been investigated. The products formed are the ax-ax diphosphate 7a and the ax-eq diphosphate 7b, with no evidence in the 31P NMR spectrum for pentacoordinate chlorooxyanionic phosphoranes 9. The structure of 7bhas been established unambiguously by NMR spectroscopy, mass spectrometry, and elemental analysis, and the structures of 5a and 7a have been confirmed by X-ray crystallography. The mechanism of the crucial diphosphate-forming reaction has been probed using 18O-labeling studies. The 18O-labeling patterns are consistent with the unsymmetric ax-eq diphosphate 7b arising from selective nucleophilic attack of the axial oxygen of 6 on the chloride 5a with inversion of configuration at phosphorus. The symmetric ax-ax diphosphate 7a can be formed directly, as a result of selective nucleophilic attack of the axial oxygen of 6 on the chloride 5a with retention of configuration, but the majority arises indirectly by isomerization of the ax-eq diphosphate 7b. The isomerization apparently involves intermolecular exchange, with nucleophilic attack of the phosphate anion 6 on the equatorially substituted phosphorus atom of 7b with inversion of configuration at phosphorus.
Collapse
Affiliation(s)
- P M Cullis
- Department of Chemistry, University of Leicester, Leicester, LE1 7RH, UK
| | | | | | | | | |
Collapse
|
37
|
Fauroux CMJ, Lee M, Cullis PM, Douglas KT, Freeman S, Gore MG. Inversion of Configuration during the Hydrolysis of d-1-Sp-myo-Inositol [17O]Thiophosphate Catalyzed by myo-Inositol Monophosphatase. J Am Chem Soc 1999. [DOI: 10.1021/ja991939r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christine M. J. Fauroux
- Department of Chemistry, The University of Leicester Leicester LE1 7RH, U.K. School of Pharmacy and Pharmaceutical Sciences Oxford Road, Manchester University Manchester M13 9PL, U.K. Division of Biochemistry and Molecular Biology School of Biological Sciences, University of Southampton, Southampton SO16 7PX, U.K
| | - Michael Lee
- Department of Chemistry, The University of Leicester Leicester LE1 7RH, U.K. School of Pharmacy and Pharmaceutical Sciences Oxford Road, Manchester University Manchester M13 9PL, U.K. Division of Biochemistry and Molecular Biology School of Biological Sciences, University of Southampton, Southampton SO16 7PX, U.K
| | - Paul M. Cullis
- Department of Chemistry, The University of Leicester Leicester LE1 7RH, U.K. School of Pharmacy and Pharmaceutical Sciences Oxford Road, Manchester University Manchester M13 9PL, U.K. Division of Biochemistry and Molecular Biology School of Biological Sciences, University of Southampton, Southampton SO16 7PX, U.K
| | - Kenneth T. Douglas
- Department of Chemistry, The University of Leicester Leicester LE1 7RH, U.K. School of Pharmacy and Pharmaceutical Sciences Oxford Road, Manchester University Manchester M13 9PL, U.K. Division of Biochemistry and Molecular Biology School of Biological Sciences, University of Southampton, Southampton SO16 7PX, U.K
| | - Sally Freeman
- Department of Chemistry, The University of Leicester Leicester LE1 7RH, U.K. School of Pharmacy and Pharmaceutical Sciences Oxford Road, Manchester University Manchester M13 9PL, U.K. Division of Biochemistry and Molecular Biology School of Biological Sciences, University of Southampton, Southampton SO16 7PX, U.K
| | - Michael G. Gore
- Department of Chemistry, The University of Leicester Leicester LE1 7RH, U.K. School of Pharmacy and Pharmaceutical Sciences Oxford Road, Manchester University Manchester M13 9PL, U.K. Division of Biochemistry and Molecular Biology School of Biological Sciences, University of Southampton, Southampton SO16 7PX, U.K
| |
Collapse
|
38
|
Cullis PM, Snip E. Stereochemical Course of Cerium(IV)-Catalyzed Hydrolysis of Cyclic Nucleotides. J Am Chem Soc 1999. [DOI: 10.1021/ja990686z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paul M. Cullis
- Contribution from the Department of Chemistry, Leicester University, Leicester, LE1 7RH, U.K
| | - Erwin Snip
- Contribution from the Department of Chemistry, Leicester University, Leicester, LE1 7RH, U.K
| |
Collapse
|
39
|
|
40
|
Florián J, Warshel A. Phosphate Ester Hydrolysis in Aqueous Solution: Associative versus Dissociative Mechanisms. J Phys Chem B 1998. [DOI: 10.1021/jp972182y] [Citation(s) in RCA: 218] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Florián
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| |
Collapse
|
41
|
|
42
|
Beaucage SL, Iyer RP. The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)87958-8] [Citation(s) in RCA: 277] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
43
|
Repke KR, Schön R. Chemistry and energetics of transphosphorylations in the mechanism of Na+/K(+)-transporting ATPase: an attempt at a unifying model. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1154:1-16. [PMID: 8389589 DOI: 10.1016/0304-4157(93)90014-f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- K R Repke
- Energy Conversion Unit, Max Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
| | | |
Collapse
|
44
|
|
45
|
Abstract
The group I intron from Tetrahymena catalyzes phosphodiester transfer reactions on various RNA substrates. A modified RNA substrate with a phosphorothioate group in one stereoisomeric form at the site of reaction was synthesized in order to determine the stereochemical course of an RNA-catalyzed reaction. The reaction product was digested with a stereospecific nuclease to determine the configuration of the product phosphorothioate. The reaction occurs with inversion of configuration at phosphorus, implying an in-line pathway for the reaction.
Collapse
Affiliation(s)
- J Rajagopal
- Department of Molecular Biology, Massachusetts General Hospital, Boston 02114
| | | | | |
Collapse
|
46
|
Feuerstein J, Goody RS, Webb MR. The Mechanism of Guanosine Nucleotide Hydrolysis by p21 c-Ha-ras. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83331-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
47
|
Juge S, Genet J. Asymmetric synthesis of phosphinates, phosphine oxides and phosphines by Michaelis Arbuzov rearrangement of chiral oxazaphospholidine. Tetrahedron Lett 1989. [DOI: 10.1016/s0040-4039(00)99124-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
48
|
Thatcher RG, Kluger R. Mechanism and Catalysis of Nucleophilic Substitution in Phosphate Esters. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 1989. [DOI: 10.1016/s0065-3160(08)60019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
|
49
|
Singh AN, Newborn J, Raushel FM. Enzymatic synthesis of uridine-5′-O-(2-thiodiphosphoglucose) and related sugar phosphorothioates. Bioorg Chem 1988. [DOI: 10.1016/0045-2068(88)90009-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
50
|
Belen'Kii L. The Literature of Heterocyclic Chemistry, Part III. ADVANCES IN HETEROCYCLIC CHEMISTRY VOLUME 44 1988. [DOI: 10.1016/s0065-2725(08)60264-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
|