2abk: Difference between revisions
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|PDB= 2abk |SIZE=350|CAPTION= <scene name='initialview01'>2abk</scene>, resolution 1.85Å | |PDB= 2abk |SIZE=350|CAPTION= <scene name='initialview01'>2abk</scene>, resolution 1.85Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=SF4:IRON/SULFUR CLUSTER'>SF4</scene> | |LIGAND= <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene> | ||
|ACTIVITY= [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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2abk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abk OCA], [http://www.ebi.ac.uk/pdbsum/2abk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2abk RCSB]</span> | |||
}} | }} | ||
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[[Category: Tainer, J A.]] | [[Category: Tainer, J A.]] | ||
[[Category: Thayer, M M.]] | [[Category: Thayer, M M.]] | ||
[[Category: dna glycosylase]] | [[Category: dna glycosylase]] | ||
[[Category: dna-repair]] | [[Category: dna-repair]] | ||
''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 01:50:30 2008'' | ||
Revision as of 01:50, 31 March 2008
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| , resolution 1.85Å | |||||||
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| Ligands: | |||||||
| Activity: | DNA-(apurinic or apyrimidinic site) lyase, with EC number 4.2.99.18 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. This structure supersedes the now removed PDB entry 1ABK. 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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