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1idx
From Proteopedia
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|PDB= 1idx |SIZE=350|CAPTION= <scene name='initialview01'>1idx</scene> | |PDB= 1idx |SIZE=350|CAPTION= <scene name='initialview01'>1idx</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |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=DU:2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>DU</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1ii1|1II1]], [[1qe7|1QE7]], [[1dgo|1DGO]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1idx OCA], [http://www.ebi.ac.uk/pdbsum/1idx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1idx RCSB]</span> | ||
}} | }} | ||
| Line 31: | Line 34: | ||
[[Category: uracil]] | [[Category: uracil]] | ||
| - | ''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 21:18:24 2008'' |
Revision as of 18:18, 30 March 2008
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| Ligands: | , , , , | ||||||
| Related: | 1II1, 1QE7, 1DGO
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structural Basis for Poor Excision from Hairpin DNA: NMR Study
Overview
Two-dimensional NMR and molecular dynamics simulations have been used to determine the three-dimensional structures of two hairpin DNA structures: d-CTAGAG GATCCUTTTGGATCCT (abbreviated as U1-hairpin) and d-CTAGAGGATCCTTUTGGATCCT (abbreviated as U3-hairpin). The 1H resonances of both of these hairpin structures have been assigned almost completely. NMR restrained molecular dynamics and energy minimization procedures have been used to describe the three-dimensional structures of these hairpins. This study and concurrent NMR structural studies on two other d-CTAGAGGA TCCTUTTGGATCCT (abbreviated as U2-hairpin) and d-CTAGAGGATCCTTTUGGATCCT (abbreviated as U4-hairpin) have shed light upon various interactions reported between Echerichia coli uracil DNA glycosylase (UDG) and uracil-containing DNA. The backbone torsion angles, which partially influence the local conformation of U12 and U14 in U1 and U3-hairpins, respectively, are probably locked in the trans conformation as in the case of U13 in the U2-hairpin. Such a stretched-out backbone conformation in the vicinity of U12 and U14 is thought to be the reason why the Km value is poor for U1- and U3-hairpins as it is for the U2-hairpin. Furthermore, the bases U12 and U14 in both U1- and U3-hairpins adopt an anti conformation, in contrast with the base conformation of U13 in the U2-hairpin, which adopts a syn conformation. The clear discrepancy observed in the U-base orientation with respect to the sugar moieties could explain why the Vmax value is 10- to 20-fold higher for the U1- and U3-hairpins compared with the U2-hairpin. Taken together, these observations support our interpretation that the unfavourable backbone results in a poor Km value, whereas the unfavourable nucleotide conformation results in a poor Vmax value. These two parameters therefore make the U1- and U3-hairpins better substrates for UDG compared with the U2-hairpin, as reported earlier [Kumar, N. V. & Varshney, U. (1997) Nucleic Acids Res. 25, 2336-2343.].
About this Structure
1IDX is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structural basis for poor uracil excision from hairpin DNA. An NMR study., Ghosh M, Rumpal N, Varshney U, Chary KV, Eur J Biochem. 2002 Apr;269(7):1886-94. PMID:11952790
Page seeded by OCA on Sun Mar 30 21:18:24 2008
