1diz
From Proteopedia
(New page: 200px<br /><applet load="1diz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1diz, resolution 2.50Å" /> '''CRYSTAL STRUCTURE OF...) |
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| - | [[Image:1diz.gif|left|200px]]<br /><applet load="1diz" size=" | + | [[Image:1diz.gif|left|200px]]<br /><applet load="1diz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1diz, resolution 2.50Å" /> | caption="1diz, resolution 2.50Å" /> | ||
'''CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA'''<br /> | '''CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The Escherichia coli AlkA protein is a base excision repair glycosylase | + | The Escherichia coli AlkA protein is a base excision repair glycosylase that removes a variety of alkylated bases from DNA. The 2.5 A crystal structure of AlkA complexed to DNA shows a large distortion in the bound DNA. The enzyme flips a 1-azaribose abasic nucleotide out of DNA and induces a 66 degrees bend in the DNA with a marked widening of the minor groove. The position of the 1-azaribose in the enzyme active site suggests an S(N)1-type mechanism for the glycosylase reaction, in which the essential catalytic Asp238 provides direct assistance for base removal. Catalytic selectivity might result from the enhanced stacking of positively charged, alkylated bases against the aromatic side chain of Trp272 in conjunction with the relative ease of cleaving the weakened glycosylic bond of these modified nucleotides. The structure of the AlkA-DNA complex offers the first glimpse of a helix-hairpin-helix (HhH) glycosylase complexed to DNA. Modeling studies suggest that other HhH glycosylases can bind to DNA in a similar manner. |
==About this Structure== | ==About this Structure== | ||
| - | 1DIZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] Full crystallographic information is available from [http:// | + | 1DIZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DIZ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Ellenberger, T | + | [[Category: Ellenberger, T E.]] |
[[Category: Hollis, T.]] | [[Category: Hollis, T.]] | ||
[[Category: Ichikawa, Y.]] | [[Category: Ichikawa, Y.]] | ||
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[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:17:00 2008'' |
Revision as of 10:17, 21 February 2008
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CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA
Overview
The Escherichia coli AlkA protein is a base excision repair glycosylase that removes a variety of alkylated bases from DNA. The 2.5 A crystal structure of AlkA complexed to DNA shows a large distortion in the bound DNA. The enzyme flips a 1-azaribose abasic nucleotide out of DNA and induces a 66 degrees bend in the DNA with a marked widening of the minor groove. The position of the 1-azaribose in the enzyme active site suggests an S(N)1-type mechanism for the glycosylase reaction, in which the essential catalytic Asp238 provides direct assistance for base removal. Catalytic selectivity might result from the enhanced stacking of positively charged, alkylated bases against the aromatic side chain of Trp272 in conjunction with the relative ease of cleaving the weakened glycosylic bond of these modified nucleotides. The structure of the AlkA-DNA complex offers the first glimpse of a helix-hairpin-helix (HhH) glycosylase complexed to DNA. Modeling studies suggest that other HhH glycosylases can bind to DNA in a similar manner.
About this Structure
1DIZ is a Single protein structure of sequence from Escherichia coli with as ligand. Active as DNA-3-methyladenine glycosylase II, with EC number 3.2.2.21 Full crystallographic information is available from OCA.
Reference
DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA., Hollis T, Ichikawa Y, Ellenberger T, EMBO J. 2000 Feb 15;19(4):758-66. PMID:10675345
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