4r8u

From Proteopedia

(Difference between revisions)

Revision as of 06:45, 2 March 2023

S-SAD structure of DINB-DNA Complex

Structural highlights

4r8u is a 6 chain structure with sequence from Escherichia coli K-12 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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

We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.

Fast native-SAD phasing for routine macromolecular structure determination.,Weinert T, Olieric V, Waltersperger S, Panepucci E, Chen L, Zhang H, Zhou D, Rose J, Ebihara A, Kuramitsu S, Li D, Howe N, Schnapp G, Pautsch A, Bargsten K, Prota AE, Surana P, Kottur J, Nair DT, Basilico F, Cecatiello V, Pasqualato S, Boland A, Weichenrieder O, Wang B, Steinmetz MO, Caffrey M, Wang M Nat Methods. 2014 Dec 15. doi: 10.1038/nmeth.3211. PMID:25506719^[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
↑ Weinert T, Olieric V, Waltersperger S, Panepucci E, Chen L, Zhang H, Zhou D, Rose J, Ebihara A, Kuramitsu S, Li D, Howe N, Schnapp G, Pautsch A, Bargsten K, Prota AE, Surana P, Kottur J, Nair DT, Basilico F, Cecatiello V, Pasqualato S, Boland A, Weichenrieder O, Wang B, Steinmetz MO, Caffrey M, Wang M. Fast native-SAD phasing for routine macromolecular structure determination. Nat Methods. 2014 Dec 15. doi: 10.1038/nmeth.3211. PMID:25506719 doi:http://dx.doi.org/10.1038/nmeth.3211

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/4r8u"

@@ Line 1: / Line 1: @@
 ==S-SAD structure of DINB-DNA Complex==
-<StructureSection load='4r8u' size='340' side='right' caption='[[4r8u]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='4r8u' size='340' side='right'caption='[[4r8u]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4r8u]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R8U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4r8u]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R8U FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0231, dinB, dinP, JW0221 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4r8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r8u OCA], [https://pdbe.org/4r8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r8u RCSB], [https://www.ebi.ac.uk/pdbsum/4r8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r8u ProSAT]</span></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=4r8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r8u OCA], [http://pdbe.org/4r8u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r8u RCSB], [http://www.ebi.ac.uk/pdbsum/4r8u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r8u ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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 ==
@@ Line 20: / Line 18: @@
 </div>
 <div class="pdbe-citations 4r8u" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Escherichia coli K-12]]
-[[Category: Ecoli]]
+[[Category: Large Structures]]
-[[Category: Kottur, J]]
+[[Category: Synthetic construct]]
-[[Category: Nair, D T]]
+[[Category: Kottur J]]
-[[Category: Oligeric, V]]
+[[Category: Nair DT]]
-[[Category: Wang, M]]
+[[Category: Oligeric V]]
-[[Category: Weinert, T]]
+[[Category: Wang M]]
-[[Category: Dna polymerase]]
+[[Category: Weinert T]]
-[[Category: Nucleotidyl transferase]]
-[[Category: Transferase-dna complex]]

4r8u

From Proteopedia

Revision as of 06:45, 2 March 2023

S-SAD structure of DINB-DNA Complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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