scholarly journals Role of nucleotidyltransferase motifs I, III and IV in the catalysis of phosphodiester bond formation by Chlorella virus DNA ligase

2002 ◽  
Vol 30 (4) ◽  
pp. 903-911 ◽  
Author(s):  
V. Sriskanda
Keyword(s):  
Bond Formation ◽  
Dna Ligase ◽  
Phosphodiester Bond ◽  
Chlorella Virus

scholarly journals Structural intermediates of a DNA–ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation

2019 ◽  
Vol 47 (14) ◽  
pp. 7147-7162 ◽  
Author(s):  
Adele Williamson ◽  
Hanna-Kirsti S Leiros
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
Bond Formation ◽  
Strand Break ◽  
Nucleophilic Attack ◽  
Dna Ligase ◽  
Phosphodiester Bond ◽  
Dna Ligases ◽  
Catalytic Metal ◽  
Ternary Structure

Abstract DNA ligases join adjacent 5′ phosphate (5′P) and 3′ hydroxyl (3′OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase–DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3′OH terminus for nucleophilic attack on the 5′P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.

scholarly journals Kinetics of T3-DNA Ligase-Catalyzed Phosphodiester Bond Formation Measured Using the α-Hemolysin Nanopore

ACS Nano ◽  
2016 ◽  
Vol 10 (12) ◽  
pp. 11127-11135 ◽  
Author(s):  
Cherie S. Tan ◽  
Jan Riedl ◽  
Aaron M. Fleming ◽  
Cynthia J. Burrows ◽  
Henry S. White
Keyword(s):  
Bond Formation ◽  
Dna Ligase ◽  
Phosphodiester Bond ◽  
Kinetics Of

Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis

2021 ◽  
Author(s):  
Sofie Dekimpe ◽  
Joleen Masschelein
Keyword(s):  
Natural Product ◽  
Bond Formation ◽  
Peptide Bond ◽  
Chemical Diversity ◽  
Peptide Bond Formation ◽  
Natural Product Biosynthesis

Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.

Topography of the Free Energy Landscape on the Claisen-Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step

2021 ◽  
Author(s):  
Nayara Dantas Coutinho ◽  
Hugo Gontijo Machado ◽  
Valter Henrique Carvalho-Silva ◽  
Wender A. Silva
Keyword(s):  
Free Energy ◽  
Temperature Effect ◽  
Strong Influence ◽  
Aldol Condensation ◽  
Energy Landscape ◽  
Bond Formation ◽  
Free Energy Landscape ◽  
Rate Controlling Step ◽  
Formation Step

Recent studies have assigned hydroxide elimination and C=C bond formation step in base-promoted aldol condensation the role of having a strong influence in the overall rate reaction, in contrast to...

Folding of peptides and proteins: role of disulfide bonds, recent developments

2013 ◽  
Vol 4 (6) ◽  
pp. 597-604 ◽  
Author(s):  
Yuji Hidaka ◽  
Shigeru Shimamoto
Keyword(s):  
Protein Folding ◽  
Disulfide Bonds ◽  
Bond Formation ◽  
Difficult Problem ◽  
Chemical Methods ◽  
Mutant Proteins ◽  
Folding Intermediates ◽  
Peptide Chemistry ◽  
Recent Developments

AbstractDisulfide-containing proteins are ideal models for studies of protein folding as the folding intermediates can be observed, trapped, and separated by HPLC during the folding reaction. However, regulating or analyzing the structures of folding intermediates of peptides and proteins continues to be a difficult problem. Recently, the development of several techniques in peptide chemistry and biotechnology has resulted in the availability of some powerful tools for studying protein folding in the context of the structural analysis of native, mutant proteins, and folding intermediates. In this review, recent developments in the field of disulfide-coupled peptide and protein folding are discussed, from the viewpoint of chemical and biotechnological methods, such as analytical methods for the detection of disulfide pairings, chemical methods for disulfide bond formation between the defined Cys residues, and applications of diselenide bonds for the regulation of disulfide-coupled peptide and protein folding.

scholarly journals Solution NMR Studies of Chlorella Virus DNA Ligase-adenylate

2010 ◽  
Vol 395 (2) ◽  
pp. 291-308 ◽  
Author(s):  
Andrea Piserchio ◽  
Pravin A. Nair ◽  
Stewart Shuman ◽  
Ranajeet Ghose
Keyword(s):  
Solution Nmr ◽  
Dna Ligase ◽  
Nmr Studies ◽  
Chlorella Virus

ChemInform Abstract: C-C Bond Formation via C-H Bond Activation under Protic Conditions: The Role of Phosphane Ligand and Cosolvent.

ChemInform ◽  
2010 ◽  
Vol 41 (18) ◽  
Author(s):  
Marc-Olivier Simon ◽  
Remi Martinez ◽  
Jean-Pierre Genet ◽  
Sylvain Darses
Keyword(s):  
Bond Activation ◽  
Bond Formation

scholarly journals Role of disulfide bond formation in the folding and assembly of the envelope glycoproteins of a pestivirus

2002 ◽  
Vol 296 (2) ◽  
pp. 470-476 ◽  
Author(s):  
Norica Branza-Nichita ◽  
Catalin Lazar ◽  
David Durantel ◽  
Raymond A Dwek ◽  
Nicole Zitzmann
Keyword(s):  
Disulfide Bond ◽  
Bond Formation ◽  
Envelope Glycoproteins ◽  
Disulfide Bond Formation
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