Investigations of kinase substrate specificity with aqua rhodium(III) complexes of adenosine 5'-triphosphate

Lu, Zuliang; Shorter, Andrew L.; Dunaway‐Mariano, Debra

doi:10.1021/bi00060a032

Cited by 5 publications

(4 citation statements)

References 42 publications

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“…The stereochemical configuration of the Mg II ATP complex is consistent with the results from studies with isomers of exchange-inert Rh III -ATP complexes (26) and with the stereoselectivity observed for nucleoside phosphorothioate substrates (27). The octahedral coordination sphere of this second Mg 2+ is completed by three water molecules.…”

Section: Resultssupporting

confidence: 83%

Structure of the Bis(Mg²⁺)−ATP−Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel^,

et al. 1998

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Pyruvate kinase from rabbit muscle has been cocrystallized as a complex with MgIIATP, oxalate, Mg2+, and either K+ or Na+. Crystals with either Na+ or K+ belong to the space group P2(1)2(1)2(1), and the asymmetric units contain two tetramers. The structures were solved by molecular replacement and refined to 2.1 (K+) and 2.35 A (Na+) resolution. The structures of the Na+ and K+ complexes are virtually isomorphous. Each of the eight subunits within the asymmetric unit contains MgIIoxalate as a bidentate complex linked to the protein through coordination of Mg2+ to the carboxylates of Glu 271 and Asp 295. Six of the subunits also contain an alpha,beta,gamma-tridentate complex of MgIIATP, and the active-site cleft, located between domains A and B, is closed in these subunits. In the remaining two subunits MgIIATP is missing, and the active-site cleft is open. Closure of the active-site cleft in the fully liganded subunits includes a rotation of 41 degrees of the B domain relative to the A domain. alpha-Carbons of residues in the B domain undergo movements of up to 17.8 A (Lys 124) in the cleft closure. Lys 206, Arg 119, and Asp 177 from the B domain move several angstroms from their positions in the open conformation to contact the MgIIATP complex in the active site. The gamma-phosphate of ATP coordinates to both magnesium ions and to the monovalent cation, K+ or Na+. A Mg2+-coordinated oxygen from the MgIIoxalate complex lies 3.0 A from Pgamma of ATP, and this oxygen is positioned for an in-line attack on the phosphorus. The side chains of Lys 269 and Arg 119 are positioned to provide leaving-group activation in the forward and reverse directions. There is no obvious candidate for the acid/base catalyst near the 2-si face of the prospective enolate of the normal substrate. A functional group linked through solvent and side-chain hydroxyls may function in a proton relay.

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Section: Resultssupporting

confidence: 83%

Structure of the Bis(Mg²⁺)−ATP−Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel^,

et al. 1998

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“…Experiments with [nO]oxalate and with the Rp and Sp epimers of [7-l70]ATP7S show that Mn2* binds at site I in this complex, where it coordinates to the pro-R oxygen of ATP7S. The a,18,7tridentate structure of the MgATP is derived from EPR results on enzyme-oxalate-Cdn-ATP-Mnn (Buchbinder & Reed, 1990), and the ¡8-, -exo configuration of the Mg11 ATP that is shown is consistent with the findings of Lu et al (1993) with a,/S,7-tridentate Rh(H20)3-ATP. The identities of ligands labeled X, X', Z, Z', and Z"are not presently known, although recent results of Lu et al (1993) make it virtually certain that the Z ligands are water molecules.…”

Section: Adosupporting

confidence: 82%

Stereochemistry of metal ion coordination to the terminal thiophosphoryl group of adenosine 5'-O-(3-thiotriphosphate) at the active site of pyruvate kinase

Buchbinder

Baraniak²,

Frey³

et al. 1993

Biochemistry

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Epimers of [gamma-17O]adenosine 5'-O-(3-thiotriphosphate) ([gamma-17O]ATP gamma S) have been used to determine the stereochemistry of Mn2+ coordination to the terminal thiophosphoryl group in complexes of pyruvate kinase, oxalate, ATP gamma S, and Mg2+, Zn2+, Co2+, or Cd2+. The complex of pyruvate kinase with oxalate and ATP binds 2 equiv of divalent cation per active site. The terminal phosphoryl group of ATP in this enzymic complex becomes a chiral center as a result of coordination to both divalent metal ions. Electron paramagnetic resonance (EPR) data for complexes of pyruvate kinase with Rp- or Sp-[gamma-17O]-ATP gamma S, [17O]oxalate, and mixtures of Mn2+ with Mg2+, Zn2+, or Co2+ show that Mn2+ binds selectively at the site defined by coordination to oxalate and the pro-R oxygen of the thiophosphoryl group of ATP gamma S. In mixtures containing Mn2+ and Cd2+ with Tl+ as the monovalent cation, two hybrid complexes form, enzyme-oxalate-MnII-ATP gamma S-CdII and enzyme-oxalate-CdII-ATP gamma S-MnII, as in the analogous complexes with ATP and K+ or Tl+ (Buchbinder, J. L., & Reed, G. H. (1990) Biochemistry 29, 1799-1806). In the enzyme-oxalate-MnII-ATP gamma S-CdII species, Mn2+ binds exclusively to the pro-R oxygen of the thiophosphoryl group. In the enzyme-oxalate-CdII-ATP gamma S-MnII species, Mn2+ binds to the pro-R oxygen (60%) and to the pro-S oxygen (40%).(ABSTRACT TRUNCATED AT 250 WORDS)

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“…nucleotide complexes have been reported for Cr(III), Co(III) (41), and Rh(III) (24). Of these, Rh(III) has been used least frequently in enzymatic studies (24,(42)(43)(44)(45), and has never been used to study polymerases. Of the three metal nucleotide complexes studied, Rh(III)-NTP has been shown to be structurally most similar to Mg-(II)NTP.…”

Section: Dna Substrates and Assay Conditions (A) Ph Sincementioning

confidence: 99%

Use of Viscogens, dNTPαS, and Rhodium(III) as Probes in Stopped-Flow Experiments To Obtain New Evidence for the Mechanism of Catalysis by DNA Polymerase β^,

et al. 2005

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The kinetic mechanism and the structural bases of the fidelity of DNA polymerases are still highly controversial. Here we report the use of three probes in the stopped-flow studies of Pol beta to obtain new, direct evidence for our previous interpretations: (a) Increasing the viscosity of the reaction buffer by sucrose or glycerol is expected to slow down the conformational change differentially, and it was shown to slow down the first (fast) fluorescence transition selectively. (b) Use of dNTPalphaS in place of dNTP is expected to slow down the chemical step preferentially, and it was shown to slow down the second (slow) fluorescence transition selectively. (c) The substitution-inert Rh(III)dNTP was used to show for the first time that the slow fluorescence change occurs after mixing of Pol beta.DNA.Rh(III)dNTP with Mg(II). These results, along with crystal structures, suggest that the subdomain-closing conformational change occurs before binding of the catalytic Mg(II) while the rate-limiting step occurs after binding of the catalytic Mg(II). These results provide new evidence to the mechanism we suggested previously, but do not support the results of three recent papers of computational studies. The results were further supported by a "sequential mixing" stopped-flow experiment that used no analogues, and thus ruled out the possibility that the discrepancy between experimental and computational results is due to the use of analogues. The methodologies can be used to examine other DNA polymerases to answer whether the properties of Pol beta are exceptional or general.

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Investigations of kinase substrate specificity with aqua rhodium(III) complexes of adenosine 5'-triphosphate

Cited by 5 publications

References 42 publications

Structure of the Bis(Mg²⁺)−ATP−Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel^,

Structure of the Bis(Mg²⁺)−ATP−Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel^,

Stereochemistry of metal ion coordination to the terminal thiophosphoryl group of adenosine 5'-O-(3-thiotriphosphate) at the active site of pyruvate kinase

Use of Viscogens, dNTPαS, and Rhodium(III) as Probes in Stopped-Flow Experiments To Obtain New Evidence for the Mechanism of Catalysis by DNA Polymerase β^,

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Investigations of kinase substrate specificity with aqua rhodium(III) complexes of adenosine 5'-triphosphate

Cited by 5 publications

References 42 publications

Structure of the Bis(Mg2+)−ATP−Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel,

Structure of the Bis(Mg2+)−ATP−Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel,

Stereochemistry of metal ion coordination to the terminal thiophosphoryl group of adenosine 5'-O-(3-thiotriphosphate) at the active site of pyruvate kinase

Use of Viscogens, dNTPαS, and Rhodium(III) as Probes in Stopped-Flow Experiments To Obtain New Evidence for the Mechanism of Catalysis by DNA Polymerase β,

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Structure of the Bis(Mg²⁺)−ATP−Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel^,

Structure of the Bis(Mg²⁺)−ATP−Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel^,

Use of Viscogens, dNTPαS, and Rhodium(III) as Probes in Stopped-Flow Experiments To Obtain New Evidence for the Mechanism of Catalysis by DNA Polymerase β^,