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5yyd

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Revision as of 09:31, 21 October 2020

DNA polymerase IV - ternary complex 15

Structural highlights

5yyd is a 6 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPO4_ECOLI] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

DNA synthesis by DNA polymerases (dPols) is central to duplication and maintenance of the genome in all living organisms. dPols catalyze the formation of a phosphodiester bond between the incoming deoxynucleoside triphosphate and the terminal primer nucleotide with the release of a pyrophosphate (PPi) group. It is believed that formation of the phosphodiester bond is an endergonic reaction and PPi has to be hydrolyzed by accompanying pyrophosphatase enzymes to ensure that the free energy change of the DNA synthesis reaction is negative and it can proceed in the forward direction. The fact that DNA synthesis proceeds in vitro in the absence of pyrophosphatases represents a long-standing conundrum regarding the thermodynamics of the DNA synthesis reaction. Using time-resolved crystallography, we show that hydrolysis of PPi is an intrinsic and critical step of the DNA synthesis reaction catalyzed by dPols. The hydrolysis of PPi occurs after the formation of the phosphodiester bond and ensures that the DNA synthesis reaction is energetically favorable without the need for additional enzymes. Also, we observe that DNA synthesis is a two Mg2+ ion assisted stepwise associative SN2 reaction. Overall, this study provides deep temporal insight regarding the primary enzymatic reaction responsible for genome duplication.

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction.,Kottur J, Nair DT Nucleic Acids Res. 2018 Jul 6;46(12):5875-5885. doi: 10.1093/nar/gky402. PMID:29850882^[6]

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

References

↑ Kim SR, Maenhaut-Michel G, Yamada M, Yamamoto Y, Matsui K, Sofuni T, Nohmi T, Ohmori H. Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA. Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13792-7. PMID:9391106
↑ Napolitano R, Janel-Bintz R, Wagner J, Fuchs RP. All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. EMBO J. 2000 Nov 15;19(22):6259-65. PMID:11080171 doi:10.1093/emboj/19.22.6259
↑ McKenzie GJ, Lee PL, Lombardo MJ, Hastings PJ, Rosenberg SM. SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol Cell. 2001 Mar;7(3):571-9. PMID:11463382
↑ Lenne-Samuel N, Wagner J, Etienne H, Fuchs RP. The processivity factor beta controls DNA polymerase IV traffic during spontaneous mutagenesis and translesion synthesis in vivo. EMBO Rep. 2002 Jan;3(1):45-9. Epub 2001 Dec 19. PMID:11751576 doi:10.1093/embo-reports/kvf007
↑ Yeiser B, Pepper ED, Goodman MF, Finkel SE. SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness. Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8737-41. Epub 2002 Jun 11. PMID:12060704 doi:10.1073/pnas.092269199
↑ Kottur J, Nair DT. Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Nucleic Acids Res. 2018 Jul 6;46(12):5875-5885. doi: 10.1093/nar/gky402. PMID:29850882 doi:http://dx.doi.org/10.1093/nar/gky402

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5yyd"

@@ Line 1: / Line 1: @@
 ==DNA polymerase IV - ternary complex 15==
-<StructureSection load='5yyd' size='340' side='right' caption='[[5yyd]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='5yyd' size='340' side='right'caption='[[5yyd]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yyd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YYD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yyd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YYD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YYD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTW:5-O-[hydroxy{[hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]thymidine'>TTW</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTW:5-O-[hydroxy{[hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]thymidine'>TTW</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5yyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyd OCA], [http://pdbe.org/5yyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yyd RCSB], [http://www.ebi.ac.uk/pdbsum/5yyd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyd ProSAT]</span></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=5yyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyd OCA], [http://pdbe.org/5yyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yyd RCSB], [http://www.ebi.ac.uk/pdbsum/5yyd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyd ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5yyd" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
@@ Line 24: / Line 27: @@
 </StructureSection>
 [[Category: DNA-directed DNA polymerase]]
+[[Category: Large Structures]]
 [[Category: Kottur, J]]
 [[Category: Nair, D T]]

5yyd

From Proteopedia

Revision as of 09:31, 21 October 2020

DNA polymerase IV - ternary complex 15

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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