1xc8
From Proteopedia
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|PDB= 1xc8 |SIZE=350|CAPTION= <scene name='initialview01'>1xc8</scene>, resolution 1.95Å | |PDB= 1xc8 |SIZE=350|CAPTION= <scene name='initialview01'>1xc8</scene>, resolution 1.95Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |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=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5'-PHOSPHATE'>FOX</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1358 Lactococcus lactis]) | |GENE= mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1358 Lactococcus lactis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1tdz|1TDZ]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://www.ebi.ac.uk/pdbsum/1xc8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB]</span> | ||
}} | }} | ||
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[[Category: Ober, M.]] | [[Category: Ober, M.]] | ||
[[Category: Zelwer, C.]] | [[Category: Zelwer, C.]] | ||
| - | [[Category: | + | [[Category: fapy]] |
| - | [[Category: | + | [[Category: glycosylase]] |
| - | [[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 Mon Mar 31 00:47:35 2008'' |
Revision as of 21:47, 30 March 2008
| |||||||
| , resolution 1.95Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Gene: | mutm, fpg (Lactococcus lactis) | ||||||
| Activity: | DNA-formamidopyrimidine glycosylase, with EC number 3.2.2.23 | ||||||
| Related: | 1TDZ
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA
Overview
Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines such as 7,8-dihydro-8-oxoguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) from damaged DNA. Here, we report the crystal structure of the Fpg protein from Lactococcus lactis (LlFpg) bound to a carbocyclic FapydG (cFapydG)-containing DNA. The structure reveals that Fpg stabilizes the cFapydG nucleoside into an extrahelical conformation inside its substrate binding pocket. In contrast to the recognition of the 8-oxodG lesion, which is bound with the glycosidic bond in a syn conformation, the cFapydG lesion displays in the complex an anti conformation. Furthermore, Fpg establishes interactions with all the functional groups of the FapyG base lesion, which can be classified in two categories: (i) those specifying a purine-derived lesion (here a guanine) involved in the Watson-Crick face recognition of the lesion and probably contributing to an optimal orientation of the pyrimidine ring moiety in the binding pocket and (ii) those specifying the imidazole ring-opened moiety of FapyG and probably participating also in the rotameric selection of the FapydG nucleobase. These interactions involve strictly conserved Fpg residues and structural water molecules mediated interactions. The significant differences between the Fpg recognition modes of 8-oxodG and FapydG provide new insights into the Fpg substrate specificity.
About this Structure
1XC8 is a Single protein structure of sequence from Lactococcus lactis. Full crystallographic information is available from OCA.
Reference
Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase., Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B, J Biol Chem. 2004 Oct 15;279(42):44074-83. Epub 2004 Jul 10. PMID:15249553
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