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Munte CE, Karl M, Kauter W, Eberlein L, Pham TV, Erlach MB, Kast SM, Kremer W, Kalbitzer HR. High pressure response of 1H NMR chemical shifts of purine nucleotides. Biophys Chem 2019; 254:106261. [PMID: 31522070 DOI: 10.1016/j.bpc.2019.106261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/01/2019] [Accepted: 09/01/2019] [Indexed: 11/25/2022]
Abstract
The study of the pressure response by NMR spectroscopy provides information on the thermodynamics of conformational equilibria in proteins and nucleic acids. For obtaining a database for expected pressure effects on free nucleotides and nucleotides bound in macromolecular complexes, the pressure response of 1H chemical shifts and J-coupling constants of the purine 5'-ribonucleotides AMP, ADP, ATP, GMP, GDP, and GTP were studied in the absence and presence of Mg2+-ions. Experiments are supported by quantum-chemical calculations of populations and chemical shift differences in order to corroborate structural interpretations and to estimate missing data for AMP. The preference of the ribose S puckering obtained from the analysis of the experimental J-couplings is also confirmed by the calculations. In addition, the pressure response of the non-hydrolysable GTP analogues GppNHp, GppCH2p, and GTPγS was examined within a pressure range up to 200 MPa. As observed earlier for 31P NMR chemical shifts of these nucleotides the pressure dependence of chemical shifts is clearly non-linear in most cases. In di- and tri-phospho nucleosides, the resonances of the two protons bound to the ribose 5' carbon are non-equivalent and can be observed separately. The gg-rotamer at C4'- C5' bond is strongly preferred and the downfield shifted resonance can be assigned to the H5″ proton in the nucleotides. In contrast, in adenosine itself the frequencies of the two resonances are interchanged.
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Affiliation(s)
- Claudia E Munte
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Matthias Karl
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Waldemar Kauter
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Lukas Eberlein
- TU Dortmund University, Physical Chemistry III, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Thuy-Vy Pham
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Markus Beck Erlach
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Stefan M Kast
- TU Dortmund University, Physical Chemistry III, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Werner Kremer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Hans Robert Kalbitzer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany.
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Ray BD, Scott J, Yan H, Nageswara Rao B. Productive versus unproductive nucleotide binding in yeast guanylate kinase mutants: comparison of R41M with K14M by proton two dimensional transferred NOESY. Biochemistry 2009; 48:5532-40. [PMID: 19419194 PMCID: PMC2772131 DOI: 10.1021/bi900139a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The R41M and K14M mutant enzymes of yeast guanylate kinase (GKy) were studied to investigate the effects of these site-directed mutations on bound-substrate conformations. Published X-ray crystal structures of yeast guanylate kinase indicate that K14 is part of the "P" loop involved in ATP and ADP binding, while R41 is suggested as a hydrogen bonding partner for the phosphoryl moiety of GMP. Both of these residues might be involved in transition state stabilization. Adenosine conformations of ATP and ADP and guanosine conformations of GMP bound to R41M and K14M mutant yeast guanylate kinase in the complexes GKy.MgATP, GKy.MgADP, and GKy.MgADP.[u-(13)C]GMP were determined by two-dimensional transferred nuclear Overhauser effect (TRNOESY) measurements combined with molecular dynamics simulations, and these conformations were compared with previously published conformations for the wild type. In the fully constrained, two substrate complexes, GKy.MgADP.[u-(13)C]GMP, the guanyl glycosidic torsion angle, chi, is 51 +/- 5 degrees for R41M and 47 +/- 5 degrees for K14M. Both are similar to the published 50 +/- 5 degrees published for wild type. For R41M with adenyl nucleotides, the glycosidic torsion angle, chi, was 55 +/- 5 degrees with MgATP, and 47 +/- 5 degrees with MgADP, which compares well to the 54 +/- 5 degrees published for wild type. However, for K14M with adenyl nucleotides, the glycosidic torsion angle was 30 +/- 5 degrees with MgATP and 28 +/- 5 degrees with MgADP. The results indicate that bound adenyl-nucleotides have significantly different conformations in the wild-type and K14M mutant enzymes, suggesting that K14 plays an important role in orienting the triphosphate of MgATP for catalysis.
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Affiliation(s)
- Bruce D. Ray
- Department of Physics, Indiana University - Purdue University at Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202-3273
| | - Joshua Scott
- Department of Physics, Indiana University - Purdue University at Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202-3273
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - B.D. Nageswara Rao
- Department of Physics, Indiana University - Purdue University at Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202-3273
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Maity H, Lin Y, Jarori GK. Structure of triphosphoryl nucleotide bound at the active site of yeast hexokinase: 1H-nuclear magnetic resonance study. JOURNAL OF PROTEIN CHEMISTRY 2002; 21:265-77. [PMID: 12168697 DOI: 10.1023/a:1019745303509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Conformation of a nonhydrolyzable adenosine triphosphate (ATP) analogue, adenylyl-(beta,gamma-methylene)-diphosphonate (AMPPCP) bound at the active site of yeast hexokinase-PII was determined by proton two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) and molecular dynamics simulations. The effect of the glucose-induced domain closure on the conformation of the nucleotide was evaluated by making measurements on two different complexes: PII AMPPCPMg(II) and PII-Glc.AMPPCPMg(Il). TRNOE measurements were made at 500 MHz, 10 degress C, as a function of several mixing times varying in the range of 40 to 200 ms. Interproton distances derived from the analysis of NOE buildup curves were used as restraints in molecular dynamics simulations to determine the conformation of the enzyme bound nucleotide. The adenosine moiety was found to bind in high anti conformation with a glycosidic torsion angle chi = 48 +/- 5 degrees in both complexes. However, significant differences in the conformations of the ribose and triphosphoryl chain of the nucleotide are observed between the two complexes. The phase angles of pseudorotation P in PII.AMPPCPMg(II) and PII.Glc.AMPPCPMg(II) are 87 degrees and 77 degrees, describing a OE and OT4 sugar pucker and the amplitudes of the sugar pucker (tau) are 37 degrees and 61 degrees, respectively.
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Affiliation(s)
- Haripada Maity
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
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Abstract
Positioning of the translation initiation complex on mRNAs requires interaction between the anticodon of initiator Met-tRNA, associated with eIF2-GTP and 40S ribosomal subunit, and the cognate start codon of the mRNA. We show that an internal ribosome entry site located in the genome of cricket paralysis virus can form 80S ribosomes without initiator Met-tRNA, eIF2, or GTP hydrolysis, with a CCU triplet in the ribosomal P site and a GCU triplet in the A site. P-site mutagenesis revealed that the P site was not decoded, and protein sequence analysis showed that translation initiates at the triplet in the A site. Translational initiation from the A site of the ribosome suggests that the repertoire of translated open reading frames in eukaryotic mRNAs may be greater than anticipated.
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Affiliation(s)
- J E Wilson
- Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305, USA
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Rao BDN. How Far Does the Itinerant Phosphoryl Group Move on a Phosphoryl-Transfer Enzyme? PHOSPHORUS SULFUR 1999. [DOI: 10.1080/10426509908546243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- B. D. Nageswara Rao
- a Department of Physics , Indiana University-Purdue University at Indianapolis , 402 N. Blackford St., Indianapolis, IN 46202–3273, USA
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