2bpf
From Proteopedia
(New page: 200px<br /><applet load="2bpf" size="450" color="white" frame="true" align="right" spinBox="true" caption="2bpf, resolution 2.900Å" /> '''STRUCTURES OF TERNA...) |
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| - | [[Image:2bpf.jpg|left|200px]]<br /><applet load="2bpf" size=" | + | [[Image:2bpf.jpg|left|200px]]<br /><applet load="2bpf" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2bpf, resolution 2.900Å" /> | caption="2bpf, resolution 2.900Å" /> | ||
'''STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP'''<br /> | '''STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA | + | Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets the reverse transcriptase of human immunodeficiency virus (HIV) and is at present used to treat AIDS. Although crystals of the two complexes belong to different space groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces. In the pol beta active site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are present in the amino acid sequences of all polymerases so far studied and are also spatially similar in the four polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal structures are now known. A two-metal ion mechanism is described for the nucleotidyl transfer reaction and may apply to all polymerases. In the ternary complex structures analyzed, pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models. |
==About this Structure== | ==About this Structure== | ||
| - | 2BPF 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 MG and DCT as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 2BPF 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=MG:'>MG</scene> and <scene name='pdbligand=DCT:'>DCT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPF OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Kumar, A.]] | [[Category: Kumar, A.]] | ||
[[Category: Pelletier, H.]] | [[Category: Pelletier, H.]] | ||
| - | [[Category: Sawaya, M | + | [[Category: Sawaya, M R.]] |
| - | [[Category: Wilson, S | + | [[Category: Wilson, S H.]] |
[[Category: DCT]] | [[Category: DCT]] | ||
[[Category: MG]] | [[Category: MG]] | ||
[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:40:12 2008'' |
Revision as of 14:40, 21 February 2008
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STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP
Overview
Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets the reverse transcriptase of human immunodeficiency virus (HIV) and is at present used to treat AIDS. Although crystals of the two complexes belong to different space groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces. In the pol beta active site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are present in the amino acid sequences of all polymerases so far studied and are also spatially similar in the four polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal structures are now known. A two-metal ion mechanism is described for the nucleotidyl transfer reaction and may apply to all polymerases. In the ternary complex structures analyzed, pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models.
About this Structure
2BPF is a Single protein structure of sequence from Rattus norvegicus with and as ligands. Full crystallographic information is available from OCA.
Reference
Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP., Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J, Science. 1994 Jun 24;264(5167):1891-903. PMID:7516580
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