2g1p
From Proteopedia
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|PDB= 2g1p |SIZE=350|CAPTION= <scene name='initialview01'>2g1p</scene>, resolution 1.89Å | |PDB= 2g1p |SIZE=350|CAPTION= <scene name='initialview01'>2g1p</scene>, resolution 1.89Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] </span> |
|GENE= dam ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= dam ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1fy3|1FY3]], [[1yfj|1YFJ]], [[1yfl|1YFL]], [[1q0t|1Q0T]], [[1q0s|1Q0S]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g1p OCA], [http://www.ebi.ac.uk/pdbsum/2g1p PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2g1p RCSB]</span> | ||
}} | }} | ||
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[[Category: Jeltsch, A.]] | [[Category: Jeltsch, A.]] | ||
[[Category: Liebert, K.]] | [[Category: Liebert, K.]] | ||
| - | [[Category: | + | [[Category: bacterial virulence factor]] |
| - | [[Category: | + | [[Category: base flipping]] |
| - | [[Category: dam methylation | + | [[Category: dam methylation]] |
| + | [[Category: gatc recognition]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:10:37 2008'' |
Revision as of 00:10, 31 March 2008
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| , resolution 1.89Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Gene: | dam (Escherichia coli) | ||||||
| Activity: | Site-specific DNA-methyltransferase (adenine-specific), with EC number 2.1.1.72 | ||||||
| Related: | 1FY3, 1YFJ, 1YFL, 1Q0T, 1Q0S
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of E. coli DNA adenine methyltransferase (DAM)
Overview
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 where it is in contact to N120.
About this Structure
2G1P is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase., Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X, J Mol Biol. 2006 Apr 28;358(2):559-70. Epub 2006 Feb 28. PMID:16524590
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