Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase

Journal of Molecular Biology
John R HortonXiaodong Cheng

Abstract

The structure of the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase in complex with cognate DNA was determined at 1.89 A resolution in the presence of S-adenosyl-L-homocysteine. DNA recognition and the dynamics of base-flipping were studied by site-directed mutagenesis, DNA methylation kinetics and fluorescence stopped-flow experiments. Our data illustrate the mechanism of coupling of DNA recognition and base-flipping. Contacts to the non-target strand in the second (3') half of the GATC site are established by R124 to the fourth base-pair, and by L122 and P134 to the third base-pair. The aromatic ring of Y119 intercalates into the DNA between the second and third base-pairs, which is essential for base-flipping to occur. Compared to previous published structures of bacteriophage T4 Dam, three major new observations are made in E.coli Dam. (1) The first Gua is recognized by K9, removal of which abrogates the first base-pair recognition. (2) The flipped target Ade binds to the surface of EcoDam in the absence of S-adenosyl-L-methionine, which illustrates a possible intermediate in the base-flipping pathway. (3) The orphaned Thy residue displays structural flexibility by adopting an extrahelical or intrahelical position ...Continue Reading

References

Mar 1, 1991·Acta Crystallographica. Section A, Foundations of Crystallography·T A JonesM Kjeldgaard
Jan 1, 1996·Annual Review of Biochemistry·P Modrich, R Lahue
Nov 26, 1996·Biochemistry·B W Allan, N O Reich
Jan 27, 1998·The Journal of Biological Chemistry·B W AllanN O Reich
Mar 21, 1998·Nucleic Acids Research·B HolzE Weinhold
Oct 3, 1998·Acta Crystallographica. Section D, Biological Crystallography·A T BrüngerG L Warren
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·F García-Del PortilloJ Casadesús
Aug 11, 2001·Science·P A Jones, D Takai
Sep 15, 2001·Nucleic Acids Research·X Cheng, R J Roberts
Apr 5, 2002·Chembiochem : a European Journal of Chemical Biology·Albert Jeltsch
Apr 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Anders Løbner-OlesenFlemming G Hansen
Aug 26, 2003·Nature Structural Biology·Zhe YangXiaodong Cheng
Jun 16, 2004·Progress in Nucleic Acid Research and Molecular Biology·Stanley Hattman, Ernst G Malygin
Jul 2, 2004·Molecular Microbiology·Michael E WatsonArnold L Smith
Apr 2, 2005·Current Opinion in Microbiology·Anders Løbner-OlesenMartin G Marinus
May 26, 2005·Protein Expression and Purification·F William Studier
Jun 15, 2005·Annual Review of Biochemistry·Mary Grace Goll, Timothy H Bestor
Jan 1, 1997·Methods in Enzymology·Liang Tong, Michael G Rossmann

❮ Previous
Next ❯

Citations

Sep 6, 2008·Nature·Hideharu HashimotoXiaodong Cheng
May 8, 2009·The Journal of Biological Chemistry·Stephanie R Coffin, Norbert O Reich
May 27, 2008·The Journal of Biological Chemistry·Stephanie R Coffin, Norbert O Reich
Jul 10, 2007·Nucleic Acids Research·Gintautas TamulaitisVirginijus Siksnys
Aug 23, 2008·Nucleic Acids Research·Michael A Carpenter, Ashok S Bhagwat
Oct 22, 2013·Nucleic Acids Research·Wil A M LoenenNoreen E Murray
Nov 4, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Makoto IwamotoHiroshi Hashimoto
Feb 2, 2010·Journal of Bacteriology·Renata Kaminska, Marjan W van der Woude
Dec 31, 2011·Molecular Endocrinology·Rui XiaoDavid D Moore
May 21, 2009·Biological Chemistry·Ernst G MalyginStanley Hattman
Aug 20, 2014·Journal of Molecular Biology·Adam J PollakNorbert O Reich
Sep 19, 2015·Wiley Interdisciplinary Reviews. Developmental Biology·Gabriel N Aughey, Tony D Southall
May 30, 2012·FEBS Letters·Pavel BashtrykovAlbert Jeltsch
Dec 15, 2015·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Lakshminarayan M IyerL Aravind
Mar 24, 2016·Nucleic Acids Research·Alexey V PindyurinBas van Steensel
Aug 24, 2006·Journal of Molecular Biology·Fa-Kuen ShiehNorbert O Reich
May 29, 2012·Chemistry & Biology·Pavel BashtrykovAlbert Jeltsch
Dec 16, 2011·Chembiochem : a European Journal of Chemical Biology·Ludovic HalbyPaola B Arimondo
May 29, 2012·Chembiochem : a European Journal of Chemical Biology·Razvan F AlbuAlbert Jeltsch
Apr 27, 2010·Nuclear Receptor Signaling·Rui XiaoDavid D Moore
Dec 30, 2006·Chembiochem : a European Journal of Chemical Biology·Philipp RathertAlbert Jeltsch
Nov 13, 2007·Angewandte Chemie·Uddhav Kumar ShigdelChuan He
Dec 13, 2007·Journal of Molecular Recognition : JMR·Rebecca L Rich, David G Myszka
Sep 3, 2009·Chembiochem : a European Journal of Chemical Biology·Hany ElsawyAlbert Jeltsch
Oct 18, 2011·Journal of Biomolecular Screening·Richard M Eglen, Terry Reisine
Jan 21, 2012·Critical Reviews in Biochemistry and Molecular Biology·Ernst G Malygin, Stanley Hattman
Sep 22, 2006·The Biochemical Journal·Shivakumara BheemanaikDesirazu N Rao
Nov 16, 2019·Nature Reviews. Microbiology·María A Sánchez-Romero, Josep Casadesús
Nov 6, 2007·The Journal of Biological Chemistry·Tomasz P JurkowskiAlbert Jeltsch
Sep 19, 2017·Frontiers in Microbiology·Amaury PayellevilleJulien Brillard
May 31, 2018·Scientific Reports·Ewa WonsTadeusz Kaczorowski

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.