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2van

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Revision as of 12:42, 23 March 2022

Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses

Structural highlights

2van is a 1 chain structure with sequence from Buffalo rat. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1bno, 1bpb, 1bpe, 1dk2, 1huo, 1huz, 1zqv, 1bnp, 1bpd, 1dk3, 1jn3, 1nom, 1rpl, 1zqu, 1zqw, 1zqx, 1zqy, 1zqz, 2bpc, 2bpf, 2bpg
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPOLB_RAT] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Understanding how DNA polymerases control fidelity requires elucidation of the mechanisms of matched and mismatched dNTP incorporations. Little is known about the latter because mismatched complexes do not crystallize readily. In this report, we employed small-angle X-ray scattering (SAXS) and structural modeling to probe the conformations of different intermediate states of mammalian DNA polymerase beta (Pol beta) in its wild-type and an error-prone variant, I260Q. Our structural results indicate that the mismatched ternary complex lies in-between the open and the closed forms, but more closely resembles the open form for WT and the closed form for I260Q. On the basis of molecular modeling, this over-stabilization of mismatched ternary complex of I260Q is likely caused by formation of a hydrogen bonding network between the side chains of Gln(260), Tyr(296), Glu(295) and Arg(258), freeing up Asp(192) to coordinate MgdNTP. These results argue against recent reports suggesting that mismatched dNTP incorporations follow a conformational path distinctly different from that of matched dNTP incorporation, or that its conformational closing is a major contributor to fidelity.

Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.,Tang KH, Niebuhr M, Tung CS, Chan HC, Chou CC, Tsai MD Nucleic Acids Res. 2008 May;36(9):2948-57. Epub 2008 Apr 2. PMID:18385153^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tang KH, Niebuhr M, Tung CS, Chan HC, Chou CC, Tsai MD. Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways. Nucleic Acids Res. 2008 May;36(9):2948-57. Epub 2008 Apr 2. PMID:18385153 doi:10.1093/nar/gkn138

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2van"

@@ Line 3: / Line 3: @@
 <StructureSection load='2van' size='340' side='right'caption='[[2van]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2van]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VAN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2van]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VAN FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1bno|1bno]], [[1bpb|1bpb]], [[1bpe|1bpe]], [[1dk2|1dk2]], [[1huo|1huo]], [[1huz|1huz]], [[1zqv|1zqv]], [[1bnp|1bnp]], [[1bpd|1bpd]], [[1dk3|1dk3]], [[1jn3|1jn3]], [[1nom|1nom]], [[1rpl|1rpl]], [[1zqu|1zqu]], [[1zqw|1zqw]], [[1zqx|1zqx]], [[1zqy|1zqy]], [[1zqz|1zqz]], [[2bpc|2bpc]], [[2bpf|2bpf]], [[2bpg|2bpg]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bno|1bno]], [[1bpb|1bpb]], [[1bpe|1bpe]], [[1dk2|1dk2]], [[1huo|1huo]], [[1huz|1huz]], [[1zqv|1zqv]], [[1bnp|1bnp]], [[1bpd|1bpd]], [[1dk3|1dk3]], [[1jn3|1jn3]], [[1nom|1nom]], [[1rpl|1rpl]], [[1zqu|1zqu]], [[1zqw|1zqw]], [[1zqx|1zqx]], [[1zqy|1zqy]], [[1zqz|1zqz]], [[2bpc|2bpc]], [[2bpf|2bpf]], [[2bpg|2bpg]]</div></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2van FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2van OCA], [http://pdbe.org/2van PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2van RCSB], [http://www.ebi.ac.uk/pdbsum/2van PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2van ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2van FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2van OCA], [https://pdbe.org/2van PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2van RCSB], [https://www.ebi.ac.uk/pdbsum/2van PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2van ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
+[[https://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 28: / Line 28: @@
 </div>
 <div class="pdbe-citations 2van" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>

2van

From Proteopedia

Revision as of 12:42, 23 March 2022

Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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