1diz
From Proteopedia
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|PDB= 1diz |SIZE=350|CAPTION= <scene name='initialview01'>1diz</scene>, resolution 2.50Å | |PDB= 1diz |SIZE=350|CAPTION= <scene name='initialview01'>1diz</scene>, resolution 2.50Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene> | + | |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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NRI:PHOSPHORIC+ACID+MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)+ESTER'>NRI</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1diz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1diz OCA], [http://www.ebi.ac.uk/pdbsum/1diz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1diz RCSB]</span> | ||
}} | }} | ||
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[[Category: Hollis, T.]] | [[Category: Hollis, T.]] | ||
[[Category: Ichikawa, Y.]] | [[Category: Ichikawa, Y.]] | ||
| - | [[Category: NA]] | ||
[[Category: 1-azaribose]] | [[Category: 1-azaribose]] | ||
[[Category: 3-methyladenine dna glycosylase]] | [[Category: 3-methyladenine dna glycosylase]] | ||
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[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:42:24 2008'' |
Revision as of 16:42, 30 March 2008
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| , resolution 2.50Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Activity: | DNA-3-methyladenine glycosylase II, with EC number 3.2.2.21 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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
Page seeded by OCA on Sun Mar 30 19:42:24 2008
