Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD +-dependent DNA ligase (LigA) Journal Article


Authors: Zhu, H.; Shuman, S.
Article Title: Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD +-dependent DNA ligase (LigA)
Abstract: NAD +-dependent DNA ligase (LigA) is essential for bacterial growth and a potential target for antimicrobial drug discovery. Here we queried the role of 14 conserved amino acids of Escherichia coli LigA by alanine scanning and thereby identified five new residues within the nucleotidyltransferase domain as being essential for LigA function in vitro and in vivo. Structure activity relationships were determined by conservative mutagenesis for the Glu-173, Arg-200, Arg-208, and Arg-277 side chains, as well as four other essential side chains that had been identified previously (Lys-115, Asp-117, Asp-285, and Lys-314). In addition, we identified Lys-290 as important for LigA activity. Reference to the structure of Enterococcus faecalis LigA allowed us to discriminate three classes of essential/important side chains that: (i) contact NAD + directly (Lys-115, Glu-173, Lys-290, and Lys-314); (ii) comprise the interface between the NMN-binding domain (domain Ia) and the nucleotidyltransferase domain or comprise part of a nick-binding site on the surface of the nucleotidyltransferase domain (Arg-200 and Arg-208); or (iii) stabilize the active site fold of the nucleotidyltransferase domain (Arg-277). Analysis of mutational effects on the isolated ligase adenylylation and phosphodiester formation reactions revealed different functions for essential side chains at different steps of the DNA ligase pathway, consistent with the proposal that the active site is serially remodeled as the reaction proceeds. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.
Keywords: controlled study; protein expression; unclassified drug; mutation; mutation, missense; nonhuman; protein conformation; protein domain; protein function; protein binding; enzyme activity; structure activity relation; structure-activity relationship; mutational analysis; time factors; cloning, molecular; dna; amino acid sequence; molecular sequence data; sequence homology, amino acid; genetic engineering; escherichia coli; binding site; amino acid; models, molecular; protein structure, tertiary; binding sites; dna mutational analysis; alanine; microbiology; polydeoxyribonucleotide synthase; glutamic acid; aspartic acid; mutagenesis; models, chemical; enzymes; glutamine; lysine; arginine; amino acid motifs; nicotinamide adenine dinucleotide; electrophoresis, polyacrylamide gel; dna ligase; dna ligases; bacterial growth; adenylation; nucleotidyltransferase; bacterial enzyme; anti-infective agents; drug products; growth kinetics; enterococcus faecalis; antimicrobial drugs; nicotinamide adenine dinucleotide dependent polydeoxyribonucleotide synthase
Journal Title: Journal of Biological Chemistry
Volume: 280
Issue: 13
ISSN: 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology  
Date Published: 2005-04-01
Start Page: 12137
End Page: 12144
Language: English
DOI: 10.1074/jbc.M413685200
PUBMED: 15671015
PROVIDER: scopus
DOI/URL:
Notes: --- - "Cited By (since 1996): 14" - "Export Date: 24 October 2012" - "CODEN: JBCHA" - "Source: Scopus"
Altmetric
Citation Impact
MSK Authors
  1. Stewart H Shuman
    504 Shuman
  2. Hui P Zhu
    14 Zhu