Molecular Basis for Nucleotide-binding Specificity: Role of the Exocyclic Amino Group “N2” in Recognition by a Guanylyl-ribonuclease

Schrift, Greta L.; Waldron, Travis T.; Timmons, Mitchell A.; Ramaswamy, S.; Kearney, William R.; Murphy, Kenneth P.

doi:10.1016/j.jmb.2005.10.019

Cited by 7 publications

(4 citation statements)

References 49 publications

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“…Instead, Lys 34 and Ser 30 interact specifically with the O3 0 atom and may discriminate dGMP with respect to GMP. Selective binding to GMP's base may arise from the recognition of its amino group by Asp 121 and Glu 88 , consistent with features of the experimental structures and similar to previous observations made on other GMP-specific systems (49).…”

Section: Specific Binding Of Gmp Atp and Mg 2dsupporting

confidence: 89%

Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase

Delalande

Sacquin-Mora

Baaden

2011

Biophysical Journal

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We investigate the conformational dynamics and mechanical properties of guanylate kinase (GK) using a multiscale approach combining high-resolution atomistic molecular dynamics and low-resolution Brownian dynamics simulations. The GK enzyme is subject to large conformational changes, leading from an open to a closed form, which are further influenced by the presence of nucleotides. As suggested by recent work on simple coarse-grained models of apo-GK, we primarily focus on GK's closure mechanism with the aim to establish a detailed picture of the hierarchy and chronology of structural events essential for the enzymatic reaction. We have investigated open-versus-closed, apo-versus-holo, and substrate-versus-product-loaded forms of the GK enzyme. Bound ligands significantly modulate the mechanical and dynamical properties of GK and rigidity profiles of open and closed states hint at functionally important differences. Our data emphasizes the role of magnesium, highlights a water channel permitting active site hydration, and reveals a structural lock that stabilizes the closed form of the enzyme.

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Section: Specific Binding Of Gmp Atp and Mg 2dsupporting

confidence: 89%

Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase

Delalande

Sacquin-Mora

Baaden

2011

Biophysical Journal

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“…Tyr42 (in RNase T1) or an arginine (in RNase Sa, barnase, and binase) has an important role in closing the guanine-binding site [10,[15][16][17]. However, although the interactions between guanine and the enzyme are highly specific, the molecular basis for guanine specificity or preference is still not completely understood [18,19].…”

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confidence: 99%

Structure of RNase Sa2 complexes with mononucleotides – new aspects of catalytic reaction and substrate recognition

et al. 2009

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Although the mechanism of RNA cleavage by RNases has been studied for many years, there remain aspects that have not yet been fully clarified. We have solved the crystal structures of RNase Sa2 in the apo form and in complexes with mononucleotides. These structures provide more details about the mechanism of RNA cleavage by RNase Sa2. In addition to Glu56 and His86, which are the principal catalytic residues, an important role in the first reaction step of RNA cleavage also seems to be played by Arg67 and Arg71, which are located in the phosphate‐binding site and form hydrogen bonds with the oxygens of the phosphate group of the mononucleotides. Their positive charge very likely causes polarization of the bonds between the oxygens and the phosphorus atom, leading to electron deficiency on the phosphorus atom and facilitating nucleophilic attack by O2′ of the ribose on the phosphorus atom, leading to cyclophosphate formation. The negatively charged Glu56 is in position to attract the proton from O2′ of the ribose. Extended molecular docking of mononucleotides, dinucleotides and trinucleotides into the active site of the enzyme allowed us to better understand the guanosine specificity of RNase Sa2 and to predict possible binding subsites for the downstream base and ribose of the second and third nucleotides. Structured digital abstract http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-7136092: RNase Sa2 (uniprotkb:http://www.ebi.uniprot.org/entry/Q53752) and RNase Sa2 (uniprotkb:http://www.ebi.uniprot.org/entry/Q53752) bind (http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0407) by x‐ray crystallography (http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0114)

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“…Recent studies have examined the thermodynamic and structural changes that occur upon protein-protein or protein-nucleic acid complexation by comparing the results of isothermal titration calorimetry (ITC) and structural analyses. [20][21][22][23][24][25][26][27][28][29][30][31][32] Thermodynamic parameters obtained using calorimetric measurements can reveal fundamental aspects of protein-protein interactions; for example, the interaction between granulocyte colony stimulating factor and its receptor is an enthalpy driven process (involving formation of favorable interactions at the molecular recognition interface), 33,34 whereas the interaction between erythropoietin and its receptor is an entropy driven process (involving the release of surface bound solvent molecules at the molecular recognition interface). 35 Interaction analysis using ITC is an effective method to quantify the thermodynamic changes associated with molecular binding interactions specific to antibody-antigen complexation, 24,[30][31][32][36][37][38][39][40][41] which typically proceeds via an enthalpy driven process.…”

Section: Introductionmentioning

confidence: 99%

An insight into the thermodynamic characteristics of human thrombopoietin complexation with TN1 antibody

et al. 2016

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Human thrombopoietin (hTPO) primarily stimulates megakaryocytopoiesis and platelet production and is neutralized by the mouse TN1 antibody. The thermodynamic characteristics of TN1 antibody-hTPO complexation were analyzed by isothermal titration calorimetry (ITC) using an antigen-binding fragment (Fab) derived from the TN1 antibody (TN1-Fab). To clarify the mechanism by which hTPO is recognized by TN1-Fab the conformation of free TN1-Fab was determined to a resolution of 2.0 Å using X-ray crystallography and compared with the hTPO-bound form of TN1-Fab determined by a previous study. This structural comparison revealed that the conformation of TN1-Fab does not substantially change after hTPO binding and a set of 15 water molecules is released from the antigen-binding site (paratope) of TN1-Fab upon hTPO complexation. Interestingly, the heat capacity change (DCp) measured by ITC (21.52 6 0.05 kJ mol 21 K 21) differed significantly from calculations based upon the X-ray structure data of the hTPO-bound and unbound forms of TN1-Fab (21.02~0.25 kJ mol 21 K 21) suggesting that hTPO undergoes an induced-fit conformational change combined with significant desolvation upon TN1-Fab binding. The results shed light on the structural biology associated with neutralizing antibody recognition.

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Molecular Basis for Nucleotide-binding Specificity: Role of the Exocyclic Amino Group “N2” in Recognition by a Guanylyl-ribonuclease

Cited by 7 publications

References 49 publications

Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase

Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase

Structure of RNase Sa2 complexes with mononucleotides – new aspects of catalytic reaction and substrate recognition

An insight into the thermodynamic characteristics of human thrombopoietin complexation with TN1 antibody

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