This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2ibt

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2ibt.gif|left|200px]]
+
{{Seed}}
 +
[[Image:2ibt.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_2ibt| PDB=2ibt | SCENE= }}
{{STRUCTURE_2ibt| PDB=2ibt | SCENE= }}
-
'''Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position'''
+
===Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position===
-
==Overview==
+
<!--
-
We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.
+
The line below this paragraph, {{ABSTRACT_PUBMED_17455934}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 17455934 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_17455934}}
==About this Structure==
==About this Structure==
Line 20: Line 24:
==Reference==
==Reference==
2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence., Lenz T, Bonnist EY, Pljevaljcic G, Neely RK, Dryden DT, Scheidig AJ, Jones AC, Weinhold E, J Am Chem Soc. 2007 May 16;129(19):6240-8. Epub 2007 Apr 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17455934 17455934]
2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence., Lenz T, Bonnist EY, Pljevaljcic G, Neely RK, Dryden DT, Scheidig AJ, Jones AC, Weinhold E, J Am Chem Soc. 2007 May 16;129(19):6240-8. Epub 2007 Apr 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17455934 17455934]
 +
 +
A Taq attack displaces bases., Blumenthal RM, Cheng X, Nat Struct Biol. 2001 Feb;8(2):101-3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11175890 11175890]
 +
 +
Differential binding of S-adenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M.TaqI., Schluckebier G, Kozak M, Bleimling N, Weinhold E, Saenger W, J Mol Biol. 1997 Jan 10;265(1):56-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8995524 8995524]
[[Category: Single protein]]
[[Category: Single protein]]
[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
Line 31: Line 39:
[[Category: Dna methyltransferase]]
[[Category: Dna methyltransferase]]
[[Category: Nucleotide flipping]]
[[Category: Nucleotide flipping]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 07:18:15 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:14:04 2008''

Revision as of 20:14, 27 July 2008

Image:2ibt.png

Template:STRUCTURE 2ibt

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position

Template:ABSTRACT PUBMED 17455934

About this Structure

2IBT is a Single protein structure of sequence from Thermus aquaticus. Full crystallographic information is available from OCA.

Reference

2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence., Lenz T, Bonnist EY, Pljevaljcic G, Neely RK, Dryden DT, Scheidig AJ, Jones AC, Weinhold E, J Am Chem Soc. 2007 May 16;129(19):6240-8. Epub 2007 Apr 25. PMID:17455934

A Taq attack displaces bases., Blumenthal RM, Cheng X, Nat Struct Biol. 2001 Feb;8(2):101-3. PMID:11175890

Differential binding of S-adenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M.TaqI., Schluckebier G, Kozak M, Bleimling N, Weinhold E, Saenger W, J Mol Biol. 1997 Jan 10;265(1):56-67. PMID:8995524

Page seeded by OCA on Sun Jul 27 23:14:04 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ibt"
Personal tools