1bpx: Difference between revisions

Revision as of 12:57, 21 February 2008

DNA POLYMERASE BETA/DNA COMPLEX

OverviewOverview

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 StructureAbout this Structure

1BPX is a Single protein structure of sequence from Homo sapiens with as ligand. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.

ReferenceReference

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 Feb 21 11:57:48 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1bpx.gif|left|200px]]<br />
+[[Image:1bpx.gif|left|200px]]<br /><applet load="1bpx" size="350" color="white" frame="true" align="right" spinBox="true"
-<applet load="1bpx" size="450" color="white" frame="true" align="right" spinBox="true"
 caption="1bpx, resolution 2.400&Aring;" />
 '''DNA POLYMERASE BETA/DNA COMPLEX'''<br />
 ==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.
+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==
-BPX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with NA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BPX OCA].
+BPX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BPX OCA].
 ==Reference==
@@ Line 18: / Line 17: @@
 [[Category: Pelletier, H.]]
 [[Category: Prasad, R.]]
-[[Category: Sawaya, M.R.]]
+[[Category: Sawaya, M R.]]
-[[Category: Wilson, S.H.]]
+[[Category: Wilson, S H.]]
 [[Category: NA]]
 [[Category: base excision repair pathway]]
@@ Line 25: / Line 24: @@
 [[Category: nucleotidyltransferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 16:13:22 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:57:48 2008''