1bpy
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1bpy.gif|left|200px]] | + | [[Image:1bpy.gif|left|200px]] |
| - | + | ||
| - | '''HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP''' | + | {{Structure |
| + | |PDB= 1bpy |SIZE=350|CAPTION= <scene name='initialview01'>1bpy</scene>, resolution 2.200Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> and <scene name='pdbligand=DCT:2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE'>DCT</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1BPY is a [ | + | 1BPY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BPY OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism., Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H, Biochemistry. 1997 Sep 16;36(37):11205-15. PMID:[http:// | + | Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism., Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H, Biochemistry. 1997 Sep 16;36(37):11205-15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9287163 9287163] |
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
| Line 25: | Line 34: | ||
[[Category: nucleotidyltransferase]] | [[Category: nucleotidyltransferase]] | ||
| - | ''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 10:14:12 2008'' |
Revision as of 08:14, 20 March 2008
| |||||||
| , resolution 2.200Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP
Overview
DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2.4 A resolution), the ternary complex including ddCTP (2.2 A), and the binary product complex containing only nicked DNA (2.6 A). Upon binding ddCTP to the binary gap complex, the thumb subdomain rotates into the closed conformation to contact the otherwise solvent-exposed ddCTP-template base pair. Thumb movement triggers further conformational changes which poise catalytic residue Asp192, dNTP, and template for nucleotidyl transfer, effectively assembling the active site. In the product nicked DNA complex, the thumb returns to the open conformation as in the gapped binary DNA complex, facilitating dissociation of the product. These findings suggest that pol beta may enhance fidelity by an induced fit mechanism in which correct base pairing between template and incoming dNTP induces alignment of catalytic groups for catalysis (via thumb closure), but incorrect base pairing will not. The structures also reveal that pol beta binds both gapped and nicked DNA with a 90 degrees kink occurring precisely at the 5'-phosphodiester linkage of the templating residue. If the DNA were not kinked in this way, contact between the thumb and dNTP-template base pair, presumably important for the checking mechanism, would be impossible, especially when the gap is but a single nucleotide. Such a 90 degrees kink may be a mechanistic feature employed by any polymerase involved in filling gaps to completion.
About this Structure
1BPY is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism., Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H, Biochemistry. 1997 Sep 16;36(37):11205-15. PMID:9287163
Page seeded by OCA on Thu Mar 20 10:14:12 2008
