1bpe: Difference between revisions

Revision as of 12:57, 21 February 2008

CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA; EVIDENCE FOR A COMMON POLYMERASE MECHANISM

OverviewOverview

Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.

About this StructureAbout this Structure

1BPE is a Single protein structure of sequence from Rattus norvegicus 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 structure of rat DNA polymerase beta: evidence for a common polymerase mechanism., Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J, Science. 1994 Jun 24;264(5167):1930-5. PMID:7516581

Page seeded by OCA on Thu Feb 21 11:57:42 2008

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OCA

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-[[Image:1bpe.gif|left|200px]]<br /><applet load="1bpe" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1bpe.gif|left|200px]]<br /><applet load="1bpe" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1bpe, resolution 2.9&Aring;" />
 '''CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA; EVIDENCE FOR A COMMON POLYMERASE MECHANISM'''<br />
 ==Overview==
-Structures of the 31-kilodalton catalytic domain of rat DNA polymerase, beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3, and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is, composed of fingers, palm, and thumb subdomains arranged to form a DNA, binding channel reminiscent of the polymerase domains of the Klenow, fragment of Escherichia coli DNA polymerase I, HIV-1 reverse, transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal, 8-kilodalton domain is attached to the fingers subdomain by a flexible, hinge. The two invariant aspartates found in all polymerase sequences and, implicated in catalytic activity have the same geometric arrangement, within structurally similar but topologically distinct palms, indicating, that the polymerases have maintained, or possibly re-evolved, a common, nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine, triphosphate in pol beta confirms the role of the invariant aspartates in, metal ion and deoxynucleoside triphosphate binding.
+Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.
 ==About this Structure==
-BPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with DTP 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=1BPE OCA].
+BPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=DTP:'>DTP</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=1BPE OCA].
 ==Reference==
@@ Line 17: / Line 17: @@
 [[Category: Kumar, A.]]
 [[Category: Pelletier, H.]]
-[[Category: Sawaya, M.R.]]
+[[Category: Sawaya, M R.]]
-[[Category: Wilson, S.H.]]
+[[Category: Wilson, S H.]]
 [[Category: DTP]]
 [[Category: nucleotidyltransferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:48:48 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:57:42 2008''