1q3f: Difference between revisions
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|PDB= 1q3f |SIZE=350|CAPTION= <scene name='initialview01'>1q3f</scene>, resolution 1.9Å | |PDB= 1q3f |SIZE=350|CAPTION= <scene name='initialview01'>1q3f</scene>, resolution 1.9Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> | |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=NRI:PHOSPHORIC+ACID+MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)+ESTER'>NRI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= UNG OR DGU OR UNG15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= UNG OR DGU OR UNG15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1emh|1EMH]], [[1ssp|1SSP]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3f OCA], [http://www.ebi.ac.uk/pdbsum/1q3f PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q3f RCSB]</span> | |||
}} | }} | ||
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==Overview== | ==Overview== | ||
The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion-uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate. | The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion-uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate. | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Seiple, L A.]] | [[Category: Seiple, L A.]] | ||
[[Category: Stivers, J T.]] | [[Category: Stivers, J T.]] | ||
[[Category: dna repair]] | [[Category: dna repair]] | ||
[[Category: udg]] | [[Category: udg]] | ||
''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 23:08:15 2008'' | ||
Revision as of 23:08, 30 March 2008
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| , resolution 1.9Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Gene: | UNG OR DGU OR UNG15 (Homo sapiens) | ||||||
| Related: | 1EMH, 1SSP
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-contianing DNA
OverviewOverview
The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion-uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate.
About this StructureAbout this Structure
1Q3F is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase., Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT, Biochemistry. 2003 Nov 4;42(43):12455-60. PMID:14580190
Page seeded by OCA on Sun Mar 30 23:08:15 2008