5c5j

From Proteopedia

(Difference between revisions)

Current revision

Poymerase Nucleotide complex

Structural highlights

5c5j is a 6 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
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

Recent studies posit that reactive oxygen species (ROS) contribute to the cell lethality of bactericidal antibiotics. However, this conjecture has been challenged and remains controversial. To resolve this controversy, we adopted a strategy that involves DNA polymerase IV (PolIV). The nucleotide pool of the cell gets oxidized by ROS and PolIV incorporates the damaged nucleotides (especially 8oxodGTP) into the genome, which results in death of the bacteria. By using a combination of structural and biochemical tools coupled with growth assays, it was shown that selective perturbation of the 8oxodGTP incorporation activity of PolIV results in considerable enhancement of the survival of bacteria in the presence of the norfloxacin antibiotic. Our studies therefore indicate that ROS induced in bacteria by the presence of antibiotics in the environment contribute significantly to cell lethality.

Reactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics.,Kottur J, Nair DT Angew Chem Int Ed Engl. 2016 Feb 12;55(7):2397-400. doi: 10.1002/anie.201509340. , Epub 2016 Jan 12. PMID:26757158^[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. Reactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics. Angew Chem Int Ed Engl. 2016 Feb 12;55(7):2397-400. doi: 10.1002/anie.201509340. , Epub 2016 Jan 12. PMID:26757158 doi:http://dx.doi.org/10.1002/anie.201509340

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/5c5j"

Categories: Escherichia coli | Large Structures | Kottur J | Nair DT

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5c5j is ON HOLD
+==Poymerase Nucleotide complex==
+<StructureSection load='5c5j' size='340' side='right'caption='[[5c5j]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5c5j]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C5J FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8GT:8-OXO-GUANOSINE-5-TRIPHOSPHATE'>8GT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5c5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c5j OCA], [https://pdbe.org/5c5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c5j RCSB], [https://www.ebi.ac.uk/pdbsum/5c5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c5j ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPO4_ECOLI 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.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Recent studies posit that reactive oxygen species (ROS) contribute to the cell lethality of bactericidal antibiotics. However, this conjecture has been challenged and remains controversial. To resolve this controversy, we adopted a strategy that involves DNA polymerase IV (PolIV). The nucleotide pool of the cell gets oxidized by ROS and PolIV incorporates the damaged nucleotides (especially 8oxodGTP) into the genome, which results in death of the bacteria. By using a combination of structural and biochemical tools coupled with growth assays, it was shown that selective perturbation of the 8oxodGTP incorporation activity of PolIV results in considerable enhancement of the survival of bacteria in the presence of the norfloxacin antibiotic. Our studies therefore indicate that ROS induced in bacteria by the presence of antibiotics in the environment contribute significantly to cell lethality.
-Authors: Nair, D.T., Kottur, J.
+Reactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics.,Kottur J, Nair DT Angew Chem Int Ed Engl. 2016 Feb 12;55(7):2397-400. doi: 10.1002/anie.201509340. , Epub 2016 Jan 12. PMID:26757158<ref>PMID:26757158</ref>
-Description: Poymerase Nucleotide complex
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Nair, D.T]]
+<div class="pdbe-citations 5c5j" style="background-color:#fffaf0;"></div>
-[[Category: Kottur, J]]
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Kottur J]]
+[[Category: Nair DT]]

5c5j

From Proteopedia

Current revision

Poymerase Nucleotide complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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