6jup - Revision history

OCA at 10:20, 22 November 2023

2023-11-22T10:20:06Z

←Older revision		Revision as of 10:20, 22 November 2023
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	<StructureSection load='6jup' size='340' side='right'caption='[[6jup]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='6jup' size='340' side='right'caption='[[6jup]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jup]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JUP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jup]] 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=6JUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JUP 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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.44Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">dinB, dbh, dinB_1, dinB_2, A8C65_11955, A9R57_12995, ACU57_05495, AML35_26730, AUQ13_19210, BANRA_02184, BANRA_03427, BET08_31995, BHS87_01175, BJJ90_21040, BMT91_15875, BUE81_28425, C5N07_13800, C9E25_22940, CA593_02435, CRM83_14635, CV83915_01335, CWS33_23695, D0X26_15110, D2185_22400, D3O91_23685, D3Y67_06560, D9D20_20085, D9D69_23735, D9E22_12045, D9F57_19765, D9H66_20200, D9H68_19465, D9I18_13635, D9J11_18290, D9J11_27145, D9J44_21795, DNQ41_05075, DTL43_23485, EAI44_14085, EAI52_15440, EC1094V2_3597, EC3234A_186c00130, EC3426_01008, EC382_20155, EC382_27145, ECTO6_03825, EEP23_17825, EFV02_01800, EFV04_12320, EFV12_23405, EFV17_17010, ERS085365_04420, ERS139211_04423, ERS150873_03537, HW43_04975, NCTC10865_04963, NCTC11022_04998, NCTC11126_03759, NCTC13148_06847, NCTC13462_02133, NCTC8985_02971, NCTC9037_04075, NCTC9045_04586, NCTC9058_02901, NCTC9062_04328, NCTC9073_03243, NCTC9117_04957, NCTC9706_01202, RK56_027425, SAMEA3472043_03017, SAMEA3472047_03125, SAMEA3472070_01946, SAMEA3484427_04943, SAMEA3484429_04916, SAMEA3752557_00095, SAMEA3752559_04620, SAMEA3753300_00345, SK85_00262, WQ89_22460, WR15_21380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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~~='~~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'>[https://proteopedia.org/fgij/fg.htm?mol=6jup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jup OCA], [https://pdbe.org/6jup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jup RCSB], [https://www.ebi.ac.uk/pdbsum/6jup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jup ProSAT]</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=6jup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jup OCA], [~~http~~://pdbe.org/6jup PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jup RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jup PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jup ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~W8STT9_ECOLX W8STT9_ECOLX]~~] 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~~.~~[SAAS:SAAS00538441] 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.~~[HAMAP-Rule~~:~~MF_01113]~~	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6jup" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jup" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Johnson~~, M K~~]]	+	[[Category: Johnson MK]]
-	[[Category: Nair~~, D T]]~~	+	[[Category: Nair DT]]
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Replication]]~~	+
-	~~[[Category: Replication-dna complex~~]]	+

OCA at 10:19, 26 February 2020

2020-02-26T10:19:50Z

←Older revision		Revision as of 10:19, 26 February 2020
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	<StructureSection load='6jup' size='340' side='right'caption='[[6jup]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='6jup' size='340' side='right'caption='[[6jup]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jup]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JUP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jup]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JUP 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>		</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dinB, dbh, dinB_1, dinB_2, A8C65_11955, A9R57_12995, ACU57_05495, AML35_26730, AUQ13_19210, BANRA_02184, BANRA_03427, BET08_31995, BHS87_01175, BJJ90_21040, BMT91_15875, BUE81_28425, C5N07_13800, C9E25_22940, CA593_02435, CRM83_14635, CV83915_01335, CWS33_23695, D0X26_15110, D2185_22400, D3O91_23685, D3Y67_06560, D9D20_20085, D9D69_23735, D9E22_12045, D9F57_19765, D9H66_20200, D9H68_19465, D9I18_13635, D9J11_18290, D9J11_27145, D9J44_21795, DNQ41_05075, DTL43_23485, EAI44_14085, EAI52_15440, EC1094V2_3597, EC3234A_186c00130, EC3426_01008, EC382_20155, EC382_27145, ECTO6_03825, EEP23_17825, EFV02_01800, EFV04_12320, EFV12_23405, EFV17_17010, ERS085365_04420, ERS139211_04423, ERS150873_03537, HW43_04975, NCTC10865_04963, NCTC11022_04998, NCTC11126_03759, NCTC13148_06847, NCTC13462_02133, NCTC8985_02971, NCTC9037_04075, NCTC9045_04586, NCTC9058_02901, NCTC9062_04328, NCTC9073_03243, NCTC9117_04957, NCTC9706_01202, RK56_027425, SAMEA3472043_03017, SAMEA3472047_03125, SAMEA3472070_01946, SAMEA3484427_04943, SAMEA3484429_04916, SAMEA3752557_00095, SAMEA3752559_04620, SAMEA3753300_00345, SK85_00262, WQ89_22460, WR15_21380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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='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=6jup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jup OCA], [http://pdbe.org/6jup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jup RCSB], [http://www.ebi.ac.uk/pdbsum/6jup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jup ProSAT]</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=6jup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jup OCA], [http://pdbe.org/6jup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jup RCSB], [http://www.ebi.ac.uk/pdbsum/6jup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jup ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:18, 19 February 2020

2020-02-19T06:18:53Z

←Older revision		Revision as of 06:18, 19 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jup is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Mutant PolIV-DNA incoming nucleotide complex==
		+	<StructureSection load='6jup' size='340' side='right'caption='[[6jup]], [[Resolution\|resolution]] 2.44Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jup]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JUP 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='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=6jup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jup OCA], [http://pdbe.org/6jup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jup RCSB], [http://www.ebi.ac.uk/pdbsum/6jup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jup ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/W8STT9_ECOLX W8STT9_ECOLX]] 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.[SAAS:SAAS00538441] 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.[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 6jup" 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

2019-06-19T04:02:18Z

←Older revision		Revision as of 04:02, 19 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2019-04-24T04:45:41Z

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

←Older revision

Revision as of 04:45, 24 April 2019

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

2019-04-24T04:45:40Z

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

New page

'''Unreleased structure'''

The entry 6jup is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]