6oiw - Revision history

OCA at 14:52, 13 March 2024

OCA — Wed, 13 Mar 2024 14:52:10 GMT

←Older revision		Revision as of 14:52, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6oiw' size='340' side='right'caption='[[6oiw]], [[Resolution\|resolution]] 3.35Å' scene=''>		<StructureSection load='6oiw' size='340' side='right'caption='[[6oiw]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6oiw]] 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=6OIW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6oiw]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OIW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=T8T:2-DEOXYGUANOSINE-5-O-(1-THIOTRIPHOSPHATE)'>T8T</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]] 3.35Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dgt, b0160, JW0156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=T8T:2-DEOXYGUANOSINE-5-O-(1-THIOTRIPHOSPHATE)'>T8T</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dGTPase dGTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.5.1 3.1.5.1] </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=6oiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oiw OCA], [https://pdbe.org/6oiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oiw RCSB], [https://www.ebi.ac.uk/pdbsum/6oiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oiw 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=6oiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oiw OCA], [~~http~~://pdbe.org/6oiw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6oiw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6oiw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6oiw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DGTP_ECOLI DGTP_ECOLI]] dGTPase preferentially hydrolyzes dGTP over the other canonical NTPs.[HAMAP-Rule:MF_00030]<ref>PMID:2826481</ref>	+	[https://www.uniprot.org/uniprot/DGTP_ECOLI DGTP_ECOLI] dGTPase preferentially hydrolyzes dGTP over the other canonical NTPs.[HAMAP-Rule:MF_00030]<ref>PMID:2826481</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli (Ec)-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec-dGTPase, including an X-ray free-electron laser structure of the free Ec-dGTPase enzyme to 3.2 A. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec-dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec-dGTPase residues at the end of the substrate-binding pocket mimic Watson-Crick interactions providing guanine base specificity, while a 7-A cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 A) of single-stranded DNA in an allosteric site primes the active site by conformationally "opening" a tyrosine gate allowing enhanced substrate binding.	+
-		+
-	The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity.,Barnes CO, Wu Y, Song J, Lin G, Baxter EL, Brewster AS, Nagarajan V, Holmes A, Soltis SM, Sauter NK, Ahn J, Cohen AE, Calero G Proc Natl Acad Sci U S A. 2019 May 7;116(19):9333-9339. doi:, 10.1073/pnas.1814999116. Epub 2019 Apr 24. PMID:31019074<ref>PMID:31019074</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6oiw" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: DGTPase]]~~	+	[[Category: Barnes CO]]
-	[[Category: Barnes~~, C O~~]]	+	[[Category: Calero G]]
-	[[Category: Calero, G]]	+	[[Category: Wu Y]]
-	[[Category: Wu, Y]]	+
-	~~[[Category: Dntp triphosphohydrolase]]~~	+
-	~~[[Category: E. coli dgtpase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Xfel~~]]	+

OCA at 07:35, 21 May 2019

OCA — Tue, 21 May 2019 07:35:22 GMT

←Older revision		Revision as of 07:35, 21 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6oiw is ~~ON HOLD~~	+	==Structure of Escherichia coli dGTPase bound to dGTP-1-thiol==
		+	<StructureSection load='6oiw' size='340' side='right'caption='[[6oiw]], [[Resolution\|resolution]] 3.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6oiw]] 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=6OIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OIW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=T8T:2-DEOXYGUANOSINE-5-O-(1-THIOTRIPHOSPHATE)'>T8T</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dgt, b0160, JW0156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dGTPase dGTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.5.1 3.1.5.1] </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=6oiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oiw OCA], [http://pdbe.org/6oiw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oiw RCSB], [http://www.ebi.ac.uk/pdbsum/6oiw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oiw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DGTP_ECOLI DGTP_ECOLI]] dGTPase preferentially hydrolyzes dGTP over the other canonical NTPs.[HAMAP-Rule:MF_00030]<ref>PMID:2826481</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli (Ec)-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec-dGTPase, including an X-ray free-electron laser structure of the free Ec-dGTPase enzyme to 3.2 A. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec-dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec-dGTPase residues at the end of the substrate-binding pocket mimic Watson-Crick interactions providing guanine base specificity, while a 7-A cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 A) of single-stranded DNA in an allosteric site primes the active site by conformationally "opening" a tyrosine gate allowing enhanced substrate binding.

-	~~Authors: Barnes, C.O~~., Wu, Y., ~~Calero~~, G.	+	The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity.,Barnes CO, Wu Y, Song J, Lin G, Baxter EL, Brewster AS, Nagarajan V, Holmes A, Soltis SM, Sauter NK, Ahn J, Cohen AE, Calero G Proc Natl Acad Sci U S A. 2019 May 7;116(19):9333-9339. doi:, 10.1073/pnas.1814999116. Epub 2019 Apr 24. PMID:31019074<ref>PMID:31019074</ref>

-	~~Description: Structure~~ of ~~Escherichia coli dGTPase bound to dGTP~~-1-~~thiol~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Barnes, C.O]]	+	<div class="pdbe-citations 6oiw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
		+	[[Category: DGTPase]]
		+	[[Category: Barnes, C O]]
	[[Category: Calero, G]]		[[Category: Calero, G]]
	[[Category: Wu, Y]]		[[Category: Wu, Y]]
		+	[[Category: Dntp triphosphohydrolase]]
		+	[[Category: E. coli dgtpase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Metalloenzyme]]
		+	[[Category: Xfel]]

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

OCA — Wed, 17 Apr 2019 04:15:55 GMT

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

←Older revision

Revision as of 04:15, 17 April 2019

OCA: New page: '''Unreleased structure''' The entry 6oiw is ON HOLD Authors: Barnes, C.O., Wu, Y., Calero, G. Description: Structure of Escherichia coli dGTPase bound to dGTP-1-thiol [[Category: Unre...

OCA — Wed, 17 Apr 2019 04:15:53 GMT

New page: '''Unreleased structure''' The entry 6oiw is ON HOLD Authors: Barnes, C.O., Wu, Y., Calero, G. Description: Structure of Escherichia coli dGTPase bound to dGTP-1-thiol [[Category: Unre...

New page

'''Unreleased structure'''

The entry 6oiw is ON HOLD

Authors: Barnes, C.O., Wu, Y., Calero, G.

Description: Structure of Escherichia coli dGTPase bound to dGTP-1-thiol
[[Category: Unreleased Structures]]
[[Category: Barnes, C.O]]
[[Category: Calero, G]]
[[Category: Wu, Y]]