2abk: Difference between revisions
New page: left|200px<br /><applet load="2abk" size="450" color="white" frame="true" align="right" spinBox="true" caption="2abk, resolution 1.85Å" /> '''REFINEMENT OF THE NA... |
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[[Image:2abk.gif|left|200px]]<br /><applet load="2abk" size=" | [[Image:2abk.gif|left|200px]]<br /><applet load="2abk" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="2abk, resolution 1.85Å" /> | caption="2abk, resolution 1.85Å" /> | ||
'''REFINEMENT OF THE NATIVE STRUCTURE OF ENDONUCLEASE III TO A RESOLUTION OF 1.85 ANGSTROM'''<br /> | '''REFINEMENT OF THE NATIVE STRUCTURE OF ENDONUCLEASE III TO A RESOLUTION OF 1.85 ANGSTROM'''<br /> | ||
==Overview== | ==Overview== | ||
The 1.85 A crystal structure of endonuclease III, combined with mutational | The 1.85 A crystal structure of endonuclease III, combined with mutational analysis, suggests the structural basis for the DNA binding and catalytic activity of the enzyme. Helix-hairpin-helix (HhH) and [4Fe-4S] cluster loop (FCL) motifs, which we have named for their secondary structure, bracket the cleft separating the two alpha-helical domains of the enzyme. These two novel DNA binding motifs and the solvent-filled pocket in the cleft between them all lie within a positively charged and sequence-conserved surface region. Lys120 and Asp138, both shown by mutagenesis to be catalytically important, lie at the mouth of this pocket, suggesting that this pocket is part of the active site. The positions of the HhH motif and protruding FCL motif, which contains the DNA binding residue Lys191, can accommodate B-form DNA, with a flipped-out base bound within the active site pocket. The identification of HhH and FCL sequence patterns in other DNA binding proteins suggests that these motifs may be a recurrent structural theme for DNA binding proteins. | ||
==About this Structure== | ==About this Structure== | ||
2ABK 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 SF4 as [http://en.wikipedia.org/wiki/ligand ligand]. This structure | 2ABK 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=SF4:'>SF4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 1ABK. Active as [http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABK OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Tainer, J | [[Category: Tainer, J A.]] | ||
[[Category: Thayer, M | [[Category: Thayer, M M.]] | ||
[[Category: SF4]] | [[Category: SF4]] | ||
[[Category: dna glycosylase]] | [[Category: dna glycosylase]] | ||
[[Category: dna-repair]] | [[Category: dna-repair]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:25:49 2008'' | ||
Revision as of 17:25, 21 February 2008
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REFINEMENT OF THE NATIVE STRUCTURE OF ENDONUCLEASE III TO A RESOLUTION OF 1.85 ANGSTROM
OverviewOverview
The 1.85 A crystal structure of endonuclease III, combined with mutational analysis, suggests the structural basis for the DNA binding and catalytic activity of the enzyme. Helix-hairpin-helix (HhH) and [4Fe-4S] cluster loop (FCL) motifs, which we have named for their secondary structure, bracket the cleft separating the two alpha-helical domains of the enzyme. These two novel DNA binding motifs and the solvent-filled pocket in the cleft between them all lie within a positively charged and sequence-conserved surface region. Lys120 and Asp138, both shown by mutagenesis to be catalytically important, lie at the mouth of this pocket, suggesting that this pocket is part of the active site. The positions of the HhH motif and protruding FCL motif, which contains the DNA binding residue Lys191, can accommodate B-form DNA, with a flipped-out base bound within the active site pocket. The identification of HhH and FCL sequence patterns in other DNA binding proteins suggests that these motifs may be a recurrent structural theme for DNA binding proteins.
About this StructureAbout this Structure
2ABK is a Single protein structure of sequence from Escherichia coli with as ligand. This structure supersedes the now removed PDB entry 1ABK. Active as DNA-(apurinic or apyrimidinic site) lyase, with EC number 4.2.99.18 Full crystallographic information is available from OCA.
ReferenceReference
Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure., Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA, EMBO J. 1995 Aug 15;14(16):4108-20. PMID:7664751
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