1pm5: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1pm5.gif|left|200px]] | [[Image:1pm5.gif|left|200px]] | ||
'''Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran containing DNA''' | {{Structure | ||
|PDB= 1pm5 |SIZE=350|CAPTION= <scene name='initialview01'>1pm5</scene>, resolution 1.95Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] | |||
|GENE= MUTM OR FPG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1358 Lactococcus lactis]) | |||
}} | |||
'''Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran containing DNA''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
1PM5 is a [ | 1PM5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PM5 OCA]. | ||
==Reference== | ==Reference== | ||
Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA., Pereira de Jesus K, Serre L, Zelwer C, Castaing B, Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:[http:// | Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA., Pereira de Jesus K, Serre L, Zelwer C, Castaing B, Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16243784 16243784] | ||
[[Category: DNA-formamidopyrimidine glycosylase]] | [[Category: DNA-formamidopyrimidine glycosylase]] | ||
[[Category: Lactococcus lactis]] | [[Category: Lactococcus lactis]] | ||
| Line 25: | Line 34: | ||
[[Category: mutm]] | [[Category: mutm]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:26:07 2008'' | ||
Revision as of 14:26, 20 March 2008
| |||||||
| , resolution 1.95Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Gene: | MUTM OR FPG (Lactococcus lactis) | ||||||
| Activity: | DNA-formamidopyrimidine glycosylase, with EC number 3.2.2.23 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran containing DNA
OverviewOverview
Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site at the 3' and 5' sides by betadelta-elimination. Here, we present the high-resolution crystal structures of the wild-type and the P1G defective mutant of Fpg from Lactococcus lactis bound to 14mer DNA duplexes containing either a tetrahydrofuran (THF) or 1,3-propanediol (Pr) AP site analogues. Structures show that THF is less extrahelical than Pr and its backbone C5'-C4'-C3' diverges significantly from those of Pr, rAP, 8-oxodG and FapydG. Clearly, the heterocyclic oxygen of THF is pushed back by the carboxylate of the strictly conserved E2 residue. We can propose that the ring-opened form of the damaged deoxyribose is the structure active form of the sugar for Fpg catalysis process. Both structural and functional data suggest that the first step of catalysis mediated by Fpg involves the expulsion of the O4' leaving group facilitated by general acid catalysis (involving E2), rather than the immediate cleavage of the N-glycosic bond of the damaged nucleoside.
About this StructureAbout this Structure
1PM5 is a Single protein structure of sequence from Lactococcus lactis. Full crystallographic information is available from OCA.
ReferenceReference
Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA., Pereira de Jesus K, Serre L, Zelwer C, Castaing B, Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:16243784
Page seeded by OCA on Thu Mar 20 13:26:07 2008