2c7q: Difference between revisions

Revision as of 21:23, 3 May 2008

HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE OUTSIDE THE RECOGNITION SEQUENCE (PAIRED WITH G) AND SAH

OverviewOverview

DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 A resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (approximately 100 ps) decay component and the large increase in the amplitude of the long (approximately 10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes that cannot be discerned from the present X-ray structures.

About this StructureAbout this Structure

2C7Q is a Protein complex structure of sequences from Haemophilus haemolyticus. Full crystallographic information is available from OCA.

ReferenceReference

Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes., Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DT, Klimasauskas S, Jones AC, Nucleic Acids Res. 2005 Dec 9;33(22):6953-60. Print 2005. PMID:16340006 Page seeded by OCA on Sat May 3 21:23:44 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:2c7q.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2c7q |SIZE=350|CAPTION= <scene name='initialview01'>2c7q</scene>, resolution 1.85&Aring;
+The line below this paragraph, containing "STRUCTURE_2c7q", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:Cit+Binding+Site+For+Chain+A'>AC1</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=5CM:5-METHYL-2&#39;-DEOXY-CYTIDINE-5&#39;-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=A1P:9-{2-DEOXY-5-O-[HYDROXY(OXIDO)PHOSPHINO]-BETA-L-ERYTHRO-PENTOFURANOSYL}-9H-PURIN-2-AMINE'>A1P</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2c7q|  PDB=2c7q  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c7q OCA], [http://www.ebi.ac.uk/pdbsum/2c7q PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2c7q RCSB]</span>
-}}
 '''HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE OUTSIDE THE RECOGNITION SEQUENCE (PAIRED WITH G) AND SAH'''
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 ==Reference==
 Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes., Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DT, Klimasauskas S, Jones AC, Nucleic Acids Res. 2005 Dec 9;33(22):6953-60. Print 2005. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16340006 16340006]
-[[Category: DNA (cytosine-5-)-methyltransferase]]
 [[Category: Haemophilus haemolyticus]]
 [[Category: Protein complex]]
 [[Category: Daujotyte, D.]]
 [[Category: Grazulis, S.]]
-[[Category: base flipping]]
+[[Category: Base flipping]]
-[[Category: dna methyltransferase]]
+[[Category: Dna methyltransferase]]
-[[Category: methyltransferase]]
+[[Category: Methyltransferase]]
-[[Category: restriction system]]
+[[Category: Restriction system]]
-[[Category: transferase]]
+[[Category: Transferase]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 21:23:44 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:17:34 2008''