OCA at 06:18, 19 February 2020

OCA — Wed, 19 Feb 2020 06:18:34 GMT

←Older revision		Revision as of 06:18, 19 February 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6jul is ~~ON HOLD until Paper~~ Publication	+	==MsDpo4-DNA complex 1==
		+	<StructureSection load='6jul' size='340' side='right'caption='[[6jul]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jul]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JUL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=6jul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jul OCA], [http://pdbe.org/6jul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jul RCSB], [http://www.ebi.ac.uk/pdbsum/6jul PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jul ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0QR77_MYCS2 A0QR77_MYCS2]] 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. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII (By similarity).[HAMAP-Rule:MF_01113]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The presence of ribonucleotides in DNA can lead to genomic instability and cellular lethality. To prevent adventitious rNTP incorporation, the majority of the DNA polymerases (dPols) possess a steric filter. The dPol named MsDpo4 (Mycobacterium smegmatis) naturally lacks this steric filter and hence is capable of rNTP addition. The introduction of the steric filter in MsDpo4 did not result in complete abrogation of the ability of this enzyme to incorporate ribonucleotides. In comparison, DNA polymerase IV (PolIV) from Escherichia coli exhibited stringent selection for deoxyribonucleotides. A comparison of MsDpo4 and PolIV led to the discovery of an additional polar filter responsible for sugar selectivity. Thr43 represents the filter in PolIV and this residue forms interactions with the incoming nucleotide to draw it closer to the enzyme surface. As a result, the 2'-OH in rNTPs will clash with the enzyme surface, and therefore ribonucleotides cannot be accommodated in the active site in a conformation compatible with productive catalysis. The substitution of the equivalent residue in MsDpo4-Cys47, with Thr led to a drastic reduction in the ability of the mycobacterial enzyme to incorporate rNTPs. Overall, our studies evince that the polar filter serves to prevent ribonucleotide incorporation by dPols.

-	~~Authors~~:	+	A polar filter in DNA polymerases prevents ribonucleotide incorporation.,Johnson MK, Kottur J, Nair DT Nucleic Acids Res. 2019 Nov 18;47(20):10693-10705. doi: 10.1093/nar/gkz792. PMID:31544946<ref>PMID:31544946</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6jul" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Johnson, M K]]
		+	[[Category: Nair, D T]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Replication]]
		+	[[Category: Replication-dna complex]]

OCA at 04:02, 19 June 2019

OCA — Wed, 19 Jun 2019 04:02:03 GMT

←Older revision		Revision as of 04:02, 19 June 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jul is ON HOLD	+	The entry 6jul is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6jul" [edit=sysop:move=sysop]

OCA — Wed, 24 Apr 2019 04:45:26 GMT

Protected "6jul" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:45, 24 April 2019

OCA: New page: '''Unreleased structure''' The entry 6jul is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 Apr 2019 04:45:25 GMT

New page: '''Unreleased structure''' The entry 6jul is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6jul is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6jul - Revision history

OCA at 06:18, 19 February 2020

OCA at 04:02, 19 June 2019

OCA: Protected "6jul" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6jul is ON HOLD Authors: Description: Category: Unreleased Structures