7yll - Revision history

OCA at 08:47, 4 March 2026

2026-03-04T08:47:27Z

← Older revision		Revision as of 08:47, 4 March 2026
Line 9:		Line 9:
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DPO4_CALS4 DPO4_CALS4] 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~~.		[https://www.uniprot.org/uniprot/DPO4_CALS4 DPO4_CALS4] Poorly processive, error-prone DNA polymerase involved in translesion repair and 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 (By similarity). Involved in translesional synthesis. Primer extension fidelity in vitro is temperature-dependent. Inserts a correct base opposite templating bases at 70 degrees Celsius, but at 37 degrees Celsius in addition to correct base pairing, base transitions, transversions and frameshifts can occur. Preferably forms erroneous base pairs C:T. Bypasses 8-oxo-dG oxidative damage by incorporating dATP or dCTP opposite of the damaged DNA template site at both temperatures in vitro (PubMed:37683741).[UniProtKB:Q47155][HAMAP-Rule:MF_01113]<ref>PMID:37683741</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	~~Translesion synthesis (TLS) is~~ a ~~kind of DNA repair that maintains the stability of the genome and ensures the normal growth of life~~ in ~~cells under emergencies. Y-family DNA polymerases~~, ~~as a kind of error-prone DNA polymerase~~, ~~mainly perform TLS~~. ~~Previous studies have suggested that the occurrence of tumors is associated with the overexpression of human DNA polymerase of the Y family~~. ~~And the combination of Y~~-~~family DNA polymerase inhibitors is promising for cancer therapy. Here we report the functional and structural characterization of a member of the Y~~-~~family DNA polymerases, TTEDbh. We determine TTEDbh is an extreme TLS polymerase that can cross~~ oxidative damage sites, and further identify the amino acids and novel structures that are critical for DNA binding, synthesis, fidelity, and oxidative damage bypass. Moreover, previously unnoticed structural elements with important functions have been discovered and analyzed. These studies provide a more experimental basis for further elucidating the ~~molecular mechanisms of~~ DNA ~~polymerase~~ in ~~the Y family. It could also shed light on the design of drugs to target tumors.~~

	~~Structure and function of extreme TLS DNA polymerase TTEDbh from Thermoanaerobacter tengcongensis.,Tian LF, Gao H, Yang S, Liu YP, Li M, Xu W, Yan XX Int J Biol Macromol. 2023 Dec 31;253~~(~~Pt 2~~)~~:126770~~. ~~doi~~: ~~, 10.1016/j.ijbiomac.2023.126770. Epub 2023 Sep 6. PMID~~:~~37683741~~<ref>PMID:37683741</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7yll" style="background-color:#fffaf0;"></div~~>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:59, 6 December 2023

2023-12-06T07:59:07Z

← Older revision		Revision as of 07:59, 6 December 2023
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7yll is ~~ON HOLD until 2025~~-01-26		==Crystal structure of TTEDbh==
			<StructureSection load='7yll' size='340' side='right'caption='[[7yll]], [[Resolution\|resolution]] 2.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[7yll]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis_MB4 Caldanaerobacter subterraneus subsp. tengcongensis MB4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YLL 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]] 2.6000092Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=7yll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yll OCA], [https://pdbe.org/7yll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yll RCSB], [https://www.ebi.ac.uk/pdbsum/7yll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yll ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/DPO4_CALS4 DPO4_CALS4] 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.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Translesion synthesis (TLS) is a kind of DNA repair that maintains the stability of the genome and ensures the normal growth of life in cells under emergencies. Y-family DNA polymerases, as a kind of error-prone DNA polymerase, mainly perform TLS. Previous studies have suggested that the occurrence of tumors is associated with the overexpression of human DNA polymerase of the Y family. And the combination of Y-family DNA polymerase inhibitors is promising for cancer therapy. Here we report the functional and structural characterization of a member of the Y-family DNA polymerases, TTEDbh. We determine TTEDbh is an extreme TLS polymerase that can cross oxidative damage sites, and further identify the amino acids and novel structures that are critical for DNA binding, synthesis, fidelity, and oxidative damage bypass. Moreover, previously unnoticed structural elements with important functions have been discovered and analyzed. These studies provide a more experimental basis for further elucidating the molecular mechanisms of DNA polymerase in the Y family. It could also shed light on the design of drugs to target tumors.

	~~Authors: Yan, X~~., Tian, L., ~~Gao, H~~.		Structure and function of extreme TLS DNA polymerase TTEDbh from Thermoanaerobacter tengcongensis.,Tian LF, Gao H, Yang S, Liu YP, Li M, Xu W, Yan XX Int J Biol Macromol. 2023 Dec 31;253(Pt 2):126770. doi: , 10.1016/j.ijbiomac.2023.126770. Epub 2023 Sep 6. PMID:37683741<ref>PMID:37683741</ref>

	~~Description~~: ~~Crystal structure of TTEDbh~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: ~~Tian, L~~]]		<div class="pdbe-citations 7yll" style="background-color:#fffaf0;"></div>
	[[Category: ~~Yan, X~~]]		== References ==
	[[Category: ~~Gao, H~~]]		<references/>
			__TOC__
			</StructureSection>
			[[Category: Caldanaerobacter subterraneus subsp. tengcongensis MB4]]
			[[Category: Large Structures]]
			[[Category: Gao H]]
			[[Category: Tian L]]
			[[Category: Yan X]]

OCA at 04:10, 6 September 2023

2023-09-06T04:10:49Z

← Older revision		Revision as of 04:10, 6 September 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7yll is ON HOLD until ~~2024~~-08-26		The entry 7yll is ON HOLD until 2025-01-26

	Authors: Yan, X., Tian, L., Gao, H.		Authors: Yan, X., Tian, L., Gao, H.

OCA at 10:37, 26 July 2023

2023-07-26T10:37:10Z

← Older revision		Revision as of 10:37, 26 July 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7yll is ON HOLD until 2024-07-26		The entry 7yll is ON HOLD until 2024-08-26

	Authors: Yan, X., Tian, L., Gao, H.		Authors: Yan, X., Tian, L., Gao, H.

OCA at 15:20, 7 September 2022

2022-09-07T15:20:04Z

← Older revision		Revision as of 15:20, 7 September 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7yll is ON HOLD		The entry 7yll is ON HOLD until 2024-07-26

	Authors: Yan, X., Tian, L., Gao, H.		Authors: Yan, X., Tian, L., Gao, H.

OCA at 03:44, 10 August 2022

2022-08-10T03:44:33Z

← Older revision		Revision as of 03:44, 10 August 2022
Line 3:		Line 3:
	The entry 7yll is ON HOLD		The entry 7yll is ON HOLD

	Authors: ~~Xiao-Xue~~, Y., ~~Li-Fei~~, T., ~~Hong-Wei~~, G.		Authors: Yan, X., Tian, L., Gao, H.

	Description: Crystal structure of TTEDbh		Description: Crystal structure of TTEDbh
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: ~~Hong-Wei~~, G]]		[[Category: Tian, L]]
	[[Category: ~~Xiao-Xue~~, Y]]		[[Category: Yan, X]]
	[[Category: ~~Li-Fei~~, T]]		[[Category: Gao, H]]

OCA: Protected "7yll" [edit=sysop:move=sysop]

2022-08-03T03:41:26Z

Protected "7yll" [edit=sysop:move=sysop]

← Older revision	Revision as of 03:41, 3 August 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7yll is ON HOLD Authors: Xiao-Xue, Y., Li-Fei, T., Hong-Wei, G. Description: Crystal structure of TTEDbh Category: Unreleased Structures [[Cate...

2022-08-03T03:41:25Z

New page: '''Unreleased structure''' The entry 7yll is ON HOLD Authors: Xiao-Xue, Y., Li-Fei, T., Hong-Wei, G. Description: Crystal structure of TTEDbh Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 7yll is ON HOLD

Authors: Xiao-Xue, Y., Li-Fei, T., Hong-Wei, G.

Description: Crystal structure of TTEDbh
[[Category: Unreleased Structures]]
[[Category: Hong-Wei, G]]
[[Category: Xiao-Xue, Y]]
[[Category: Li-Fei, T]]