2xca

From Proteopedia

(Difference between revisions)

Revision as of 17:42, 25 December 2014

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dGTP - MAGNESIUM FORM

Structural highlights

2xca is a 3 chain structure with sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:	,
Related:	2asl, 1s0m, 2jeg, 1rys, 2v4s, 2j6t, 2w9b, 1n56, 1jx4, 2atl, 2c22, 2va2, 1s97, 2agq, 2jej, 2w9c, 2asj, 2ago, 2w9a, 2asd, 1jxl, 1n48, 2bq3, 2uvu, 2j6u, 2agp, 2c2r, 1s0n, 1s0o, 2jef, 2w8l, 2uvw, 2bqr, 2jei, 1s9f, 2au0, 2bqu, 2c28, 2v9w, 2v4r, 2c2e, 1ryr, 2uvv, 2c2d, 2v4q, 2br0, 1s10, 2j6s, 2uvr, 2va3, 2w8k, 2v4t, 2xc9, 2xcp
Gene:	DPO4 (Sulfolobus solfataricus)
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[DPO42_SULSO] 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. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]

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

Crystal structures of a binary Mg2+-form Dpo4-DNA complex with 1,N2-etheno-dG in the template strand as well as of ternary Mg2+-form Dpo4-DNA-dCTP/dGTP complexes with 8-oxoG in the template strand have been determined. Comparison of their conformations and active-site geometries with those of the corresponding Ca2+-form complexes revealed that the DNA and polymerase undergo subtle changes as a result of the catalytically more active Mg2+ occupying both the A and B sites.

Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus.,Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Sep 1;66(Pt, 9):1013-8. Epub 2010 Aug 21. PMID:20823515^[1]

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

References

↑ Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M. Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Sep 1;66(Pt, 9):1013-8. Epub 2010 Aug 21. PMID:20823515 doi:10.1107/S1744309110029374

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2xca]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XCA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XCA FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2asl|2asl]], [[1s0m|1s0m]], [[2jeg|2jeg]], [[1rys|1rys]], [[2v4s|2v4s]], [[2j6t|2j6t]], [[2w9b|2w9b]], [[1n56|1n56]], [[1jx4|1jx4]], [[2atl|2atl]], [[2c22|2c22]], [[2va2|2va2]], [[1s97|1s97]], [[2agq|2agq]], [[2jej|2jej]], [[2w9c|2w9c]], [[2asj|2asj]], [[2ago|2ago]], [[2w9a|2w9a]], [[2asd|2asd]], [[1jxl|1jxl]], [[1n48|1n48]], [[2bq3|2bq3]], [[2uvu|2uvu]], [[2j6u|2j6u]], [[2agp|2agp]], [[2c2r|2c2r]], [[1s0n|1s0n]], [[1s0o|1s0o]], [[2jef|2jef]], [[2w8l|2w8l]], [[2uvw|2uvw]], [[2bqr|2bqr]], [[2jei|2jei]], [[1s9f|1s9f]], [[2au0|2au0]], [[2bqu|2bqu]], [[2c28|2c28]], [[2v9w|2v9w]], [[2v4r|2v4r]], [[2c2e|2c2e]], [[1ryr|1ryr]], [[2uvv|2uvv]], [[2c2d|2c2d]], [[2v4q|2v4q]], [[2br0|2br0]], [[1s10|1s10]], [[2j6s|2j6s]], [[2uvr|2uvr]], [[2va3|2va3]], [[2w8k|2w8k]], [[2v4t|2v4t]], [[2xc9|2xc9]], [[2xcp|2xcp]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2asl|2asl]], [[1s0m|1s0m]], [[2jeg|2jeg]], [[1rys|1rys]], [[2v4s|2v4s]], [[2j6t|2j6t]], [[2w9b|2w9b]], [[1n56|1n56]], [[1jx4|1jx4]], [[2atl|2atl]], [[2c22|2c22]], [[2va2|2va2]], [[1s97|1s97]], [[2agq|2agq]], [[2jej|2jej]], [[2w9c|2w9c]], [[2asj|2asj]], [[2ago|2ago]], [[2w9a|2w9a]], [[2asd|2asd]], [[1jxl|1jxl]], [[1n48|1n48]], [[2bq3|2bq3]], [[2uvu|2uvu]], [[2j6u|2j6u]], [[2agp|2agp]], [[2c2r|2c2r]], [[1s0n|1s0n]], [[1s0o|1s0o]], [[2jef|2jef]], [[2w8l|2w8l]], [[2uvw|2uvw]], [[2bqr|2bqr]], [[2jei|2jei]], [[1s9f|1s9f]], [[2au0|2au0]], [[2bqu|2bqu]], [[2c28|2c28]], [[2v9w|2v9w]], [[2v4r|2v4r]], [[2c2e|2c2e]], [[1ryr|1ryr]], [[2uvv|2uvv]], [[2c2d|2c2d]], [[2v4q|2v4q]], [[2br0|2br0]], [[1s10|1s10]], [[2j6s|2j6s]], [[2uvr|2uvr]], [[2va3|2va3]], [[2w8k|2w8k]], [[2v4t|2v4t]], [[2xc9|2xc9]], [[2xcp|2xcp]]</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPO4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPO4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</td></tr>
-<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2xca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xca OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xca RCSB], [http://www.ebi.ac.uk/pdbsum/2xca PDBsum]</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=2xca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xca OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xca RCSB], [http://www.ebi.ac.uk/pdbsum/2xca PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/DPO42_SULSO DPO42_SULSO]] 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. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 39: @@
 [[Category: DNA-directed DNA polymerase]]
 [[Category: Sulfolobus solfataricus]]
-[[Category: Egli, M.]]
+[[Category: Egli, M]]
-[[Category: Irimia, A.]]
+[[Category: Irimia, A]]
 [[Category: Transferase-dna complex]]
 [[Category: Translesion nucleotidyltransferase]]

2xca

From Proteopedia

Revision as of 17:42, 25 December 2014

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dGTP - MAGNESIUM FORM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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