Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine

Tran, Phidung H; Korszun, Z. R.; Cerritelli, Susana M.; Springhorn, Sylvia S.; Lacks, Sanford A.

doi:10.1016/s0969-2126(98)00154-3

Cited by 84 publications

(70 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Remarkably, the invariant Asp-Pro-Pro-Tyr of T4Dam is superimposable onto the corresponding motif in the ternary complex of M.TaqI 23 (Fig. 2e), as well as the binary complex of M.DpnII 26 and M.RsrI 27 in the absence of DNA, suggesting that the conformation of Asp-Pro-Pro-Tyr is quite stable and highly conserved. In addition, an invariant Lys11 (motif X) interacts with Asp171 (via charge-charge interaction) and Tyr174 (via hydrogen bond) (Fig.…”

Section: Active Sitementioning

confidence: 94%

“…The same closed-flap AdoHcy binding site is observed in the nonspecific ternary structure (see below); in both cases, the 3 10 -helix and the flanking loops are not involved in any crystal packing contacts. An open conformation was observed in the binary M.DpnII-AdoMet structure 26 , where the AdoMet is largely visible and the cover (a five-residue longer loop after strand β4) is opened up (Fig. 2d).…”

Section: Dam-adohcy Interactionsmentioning

confidence: 96%

“…21 . Dashed lines show the unstructured regions: the loop between strands β6 and β7 is disordered in both the binary and ternary structures of T4Dam, as well as in the M.DpnII-AdoMet structure 26 . T4Dam was susceptible to proteolysis near residue 250 within this loop (data not shown).…”

Section: Coordinatesmentioning

confidence: 99%

“…The solution of several MTase crystal structures, M.HhaI 22 , M.TaqI 23 , M.HaeIII 24 , M.PvuII 25 , M.DpnII 26 and M.RsrI 27 , has contributed essential details related to the specific protein-DNA and protein-cofactor interactions. As a preliminary step to the potential design of Dam inhibitors, we have characterized two structures containing the Dam MTase encoded by bacteriophage T4: one in a binary complex with AdoHcy, and the second in a ternary complex with both AdoHcy and a synthetic 12-bp DNA duplex.…”

mentioning

confidence: 99%

See 3 more Smart Citations

Structure of the bacteriophage T4 DNA adenine methyltransferase

Yang

Horton

Zhou

et al. 2003

Nat Struct Mol Biol

View full text Add to dashboard Cite

DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene expression as well as bacterial virulence. We report here the crystal structures of the bacteriophage T4Dam DNA adenine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a seven-stranded catalytic domain that harbors the binding site for AdoHcy and a DNA binding domain consisting of a five-helix bundle and a β-hairpin that is conserved in the family of GATC-related MTase orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a nonspecific mode that contained two Dam monomers per synthetic duplex, even though the DNA contains a single GATC site. The ternary structure provides a rare snapshot of an enzyme poised for linear diffusion along the DNA.DNA MTases catalyze methyl group transfer from donor S-adenosyl-L-methionine (AdoMet), producing S-adenosyl-L-homocysteine (AdoHcy) and methylated DNA. Although most prokaryote DNA MTases are components of restriction-modification systems, some MTases are not associated with cognate restriction enzymes, such as the Escherichia coli DNA adenine MTase (Dam). This enzyme methylates an exocyclic amino nitrogen (N6) of the adenine in GATC 1,2 . Dam MTase gene orthologs are widespread among enteric bacteria and their bacteriophages (see Fig. 1 legend). Dam methylation is not essential for the viability of E. coli, unless it is combined with certain other mutations 3 ; however, Dam is an essential gene in Vibrio cholerae and Yersinia pesudotuberculosis, at least under the tested growth conditions 4 . Dam methylation is essential for the virulence of Salmonella serovar typhimurium in a murine model of typhoid fever [5][6][7] . These observations COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. NIH Public Access RESULTS Overall structure of DamThe monomeric Dam structure contains 9 β-strands and 11 α-helices (Fig. 1). The Nterminal region (residues 1-52) and C-terminal region (residues 149-259) come together, forming the catalytic domain (green in Figs. 1 and 2a) with a seven-stranded β-sheet, a characteristic feature of the class-I AdoMet-dependent MTases 28 . The N-terminal helices αZ and αA are located on one side of the β-sheet, and helices αC, αD1 and αD2 and αE are on the other side. Between strands β2 and β3 is a separate domain, which we designate as the target-recognition domain (TRD). TRD is composed of a five-helix bundle (αB1-αB5) (yellow in Figs. 1 and 2a) and a 25-residue segment containing a β-hairpin (β8 and β9) inserted between helices αB4 and αB5 (red). The overall dimensions of the molecule are 55 × 34 × 28 Å, with an open cleft located between the catalytic domain (green) and the TRD (yellow and red). Conserved residues and the effects of mutationsBased on the linear arrangement of conserved motifs in DNA MTases, T4Dam is classified in the...

show abstract

Section: Active Sitementioning

confidence: 94%

Section: Dam-adohcy Interactionsmentioning

confidence: 96%

Section: Coordinatesmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Structure of the bacteriophage T4 DNA adenine methyltransferase

Yang

Horton

Zhou

et al. 2003

Nat Struct Mol Biol

View full text Add to dashboard Cite

show abstract

“…Methyltransferases have perhaps evolved from dehydrogenases, with their structural fold being highly conserved, followed by function and, last, sequence (17,30). M.HhaI shares an AdoMet binding site architecture (Rossman fold) as found in the cofactor binding site of NADPH dependent enzymes (16).…”

Section: Cation-interaction Is Not Involved In the Origin Of Dual Modmentioning

confidence: 99%

Water-assisted Dual Mode Cofactor Recognition by HhaI DNA Methyltransferase

Swaminathan¹,

Sankpal²,

Rao³

et al. 2002

Journal of Biological Chemistry

View full text Add to dashboard Cite

Methyltransferase-catalyzed modification of substrate DNA, RNA, or protein serves as a key signal in the regulation and maintenance of diverse biological processes in a range of organisms from prokaryotes to eukaryotes (1, 2). Subsequent to its isolation from Hemophilus haemolyticus nearly a quarter century ago, HhaI DNA methyltransferase (M.HhaI) 1 has been subjected to incisive investigations yielding detailed insights into the reaction chemistry (3-7). M.HhaI is an S-adenosyl-Lmethionine (AdoMet) dependent DNA methyltransferase that catalyzes the covalent attachment of a methyl group at the C-5 position of the aromatic ring of the first cytosine in the specific sequence 5Ј-GCGC-3Ј. Its ability to perform the methyl transfer within the B-DNA helix was rationalized by a localized "DNA backbone rotation" by nearly 180°(base flipping) without significantly bending or kinking of the rest of the duplex (8 -11). Base flipping serves to deliver the base into a concave catalytic site in the enzyme (8). The Gln 287 side chain fills up the gap generated concomitantly in the DNA bound with M.HhaI, leading to a stable and specific interruption of the aromatic -stacked base pairs, a feature recently utilized to evaluate long range electron migration through DNA (12). M.HhaI methylates all of the cytosines in poly(dG-dC) DNA (3), with hemimethylated DNA being the preferred substrate (13). Both the reaction product S-adenosyl-L-homocysteine (AdoHcy) (14) and, by implication, the cofactor AdoMet (7), appear to share the ability to drive M.HhaI to trap the target cytosine in the catalytic site to form a productive complex. These results portray AdoMet and AdoHcy as important modulators of the multiple binding modes of the DNA-bound enzyme.Despite a wealth of information on the structural, dynamic, and kinetic aspects of the M.HhaI mechanism, little attention has been paid to the energetics of AdoMet and AdoHcy recognition reactions. No molecule other than ATP serves as a cofactor in more diverse reactions than does AdoMet (15). It was, therefore, of interest to understand the thermodynamic basis of recognition of the ubiquitous cofactor AdoMet by methyltransferases, a feature shared among structurally related enzymes that catalyze reactions with diverse substrate specificities (16 -18). For example, a snapshot of a step that follows methyl transfer has been elucidated by crystallographic analyses of the DNA intermediate covalently bound to M.HhaI (8) and M.HaeIII (19). Despite its absence in the original crystallization mix of the ternary complex, it was AdoHcy that was found, fortuitously, to reside within the cofactor binding pocket (8) shared by AdoMet (16). This illustrates that the transfer of the methyl group from AdoMet to the target cytosine results in the formation not only of the modified (i.e. methylated) DNA but also the transformation of AdoMet into AdoHcy. On the other * This work was supported by grants from the Department of Biotechnology, Government of India (to D. N. R. and A. S.) and the Department of Scien...

show abstract

Structural characterization of two tandemly arranged DNA methyltransferase genes fromNeisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P

1999

View full text Add to dashboard Cite

Two adjacent genes encoding DNA methyltransferases (MTases) of Neisseria gonorrhoeae MS11, an active N4-cytosine specific M. NgoMXV and an inactive 5-cytosine type M. NgoMorf2P, were cloned into Escherichia coli and sequenced. We analyzed the deduced amino acid sequence of both gene products and localized conserved regions characteristic for DNA MTases. Structure prediction, threading-derived alignments, and comparison with the common fold for DNA MTases allowed for construction of super-secondary and tertiary models for M.NgoMorf2P and M.NgoMXV, respectively. These models helped in identification of amino acids and structural elements essential for function of both enzymes. The implications of this putative structural model on the catalytic mechanism of M.NgoMXV and its possible relation to the common ancestor of modern DNA amino-MTases are also discussed.

show abstract

Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine

Cited by 84 publications

References 68 publications

Structure of the bacteriophage T4 DNA adenine methyltransferase

Structure of the bacteriophage T4 DNA adenine methyltransferase

Water-assisted Dual Mode Cofactor Recognition by HhaI DNA Methyltransferase

Structural characterization of two tandemly arranged DNA methyltransferase genes fromNeisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P

Contact Info

Product

Resources

About