6vcq - Revision history

OCA at 08:09, 11 October 2023

OCA — Wed, 11 Oct 2023 08:09:11 GMT

←Older revision		Revision as of 08:09, 11 October 2023
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	<StructureSection load='6vcq' size='340' side='right'caption='[[6vcq]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6vcq' size='340' side='right'caption='[[6vcq]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vcq]] is a 1 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=6VCQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VCQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vcq]] is a 1 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=6VCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VCQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GTP:GUANOSINE~~-~~5-TRIPHOSPHATE'>GTP</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6vcn\|6vcn]], [[6vco\|6vco]], [[6vcp\|6vcp]], [[6vck\|6vck]], [[6vcl\|6vcl]], [[6vcm\|6vcm]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">rppH, nudH, ygdP, b2830, JW2798 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=6vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vcq OCA], [https://pdbe.org/6vcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vcq RCSB], [https://www.ebi.ac.uk/pdbsum/6vcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vcq ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vcq OCA], [~~http~~://pdbe.org/6vcq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vcq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vcq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vcq ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RPPH_ECOLI RPPH_ECOLI]] Master regulator of 5'-dependent mRNA decay. Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Preferentially hydrolyzes diadenosine penta-phosphate with ATP as one of the reaction products. Also able to hydrolyze diadenosine hexa- and tetra-phosphate. Has no activity on diadenosine tri-phosphate, ADP-ribose, NADH and UDP-glucose. In the meningitis causing strain E.coli K1, has been shown to play a role in HBMEC (human brain microvascular endothelial cells) invasion in vitro.<ref>PMID:10760174</ref> <ref>PMID:18202662</ref>	+	[https://www.uniprot.org/uniprot/RPPH_ECOLI RPPH_ECOLI] Master regulator of 5'-dependent mRNA decay. Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Preferentially hydrolyzes diadenosine penta-phosphate with ATP as one of the reaction products. Also able to hydrolyze diadenosine hexa- and tetra-phosphate. Has no activity on diadenosine tri-phosphate, ADP-ribose, NADH and UDP-glucose. In the meningitis causing strain E.coli K1, has been shown to play a role in HBMEC (human brain microvascular endothelial cells) invasion in vitro.<ref>PMID:10760174</ref> <ref>PMID:18202662</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Duan, W]]	+	[[Category: Duan W]]
-	[[Category: Gao, A]]	+	[[Category: Gao A]]
-	[[Category: Kaushik, A]]	+	[[Category: Kaushik A]]
-	[[Category: Serganov, A]]	+	[[Category: Serganov A]]
-	[[Category: Vasilyev, N]]	+	[[Category: Vasilyev N]]
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna degradation~~]]	+

OCA at 06:12, 22 April 2020

OCA — Wed, 22 Apr 2020 06:12:04 GMT

←Older revision		Revision as of 06:12, 22 April 2020
Line 3:		Line 3:
	<StructureSection load='6vcq' size='340' side='right'caption='[[6vcq]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6vcq' size='340' side='right'caption='[[6vcq]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vcq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6VCQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vcq]] is a 1 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=6VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VCQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6vcn\|6vcn]], [[6vco\|6vco]], [[6vcp\|6vcp]], [[6vck\|6vck]], [[6vcl\|6vcl]], [[6vcm\|6vcm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6vcn\|6vcn]], [[6vco\|6vco]], [[6vcp\|6vcp]], [[6vck\|6vck]], [[6vcl\|6vcl]], [[6vcm\|6vcm]]</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=6vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vcq OCA], [http://pdbe.org/6vcq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vcq RCSB], [http://www.ebi.ac.uk/pdbsum/6vcq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vcq ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rppH, nudH, ygdP, b2830, JW2798 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vcq OCA], [http://pdbe.org/6vcq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vcq RCSB], [http://www.ebi.ac.uk/pdbsum/6vcq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vcq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Duan, W]]		[[Category: Duan, W]]

OCA at 08:17, 5 February 2020

OCA — Wed, 05 Feb 2020 08:17:52 GMT

←Older revision		Revision as of 08:17, 5 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vcq is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of E.coli RppH in complex with GTP==
		+	<StructureSection load='6vcq' size='340' side='right'caption='[[6vcq]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6vcq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VCQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6vcn\|6vcn]], [[6vco\|6vco]], [[6vcp\|6vcp]], [[6vck\|6vck]], [[6vcl\|6vcl]], [[6vcm\|6vcm]]</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=6vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vcq OCA], [http://pdbe.org/6vcq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vcq RCSB], [http://www.ebi.ac.uk/pdbsum/6vcq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vcq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPPH_ECOLI RPPH_ECOLI]] Master regulator of 5'-dependent mRNA decay. Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Preferentially hydrolyzes diadenosine penta-phosphate with ATP as one of the reaction products. Also able to hydrolyze diadenosine hexa- and tetra-phosphate. Has no activity on diadenosine tri-phosphate, ADP-ribose, NADH and UDP-glucose. In the meningitis causing strain E.coli K1, has been shown to play a role in HBMEC (human brain microvascular endothelial cells) invasion in vitro.<ref>PMID:10760174</ref> <ref>PMID:18202662</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	All enzymes face a challenge of discriminating cognate substrates from similar cellular compounds. Finding a correct substrate is especially difficult for the Escherichia coli Nudix hydrolase RppH, which triggers 5'-end-dependent RNA degradation by removing orthophosphate from the 5'-diphosphorylated transcripts. Here we show that RppH binds and slowly hydrolyzes NTPs, NDPs and (p)ppGpp, which each resemble the 5'-end of RNA. A series of X-ray crystal structures of RppH-nucleotide complexes, trapped in conformations either compatible or incompatible with hydrolysis, explain the low reaction rates of mononucleotides and suggest two distinct mechanisms for their hydrolysis. While RppH adopts the same catalytic arrangement with 5'-diphosphorylated nucleotides as with RNA, the enzyme hydrolyzes 5'-triphosphorylated nucleotides by extending the active site with an additional Mg2+ cation, which coordinates another reactive nucleophile. Although the average intracellular pH minimizes the hydrolysis of nucleotides by slowing their reaction with RppH, they nevertheless compete with RNA for binding and differentially inhibit the reactivity of RppH with triphosphorylated and diphosphorylated RNAs. Thus, E. coli RppH integrates various signals, such as competing non-cognate substrates and a stimulatory protein factor DapF, to achieve the differential degradation of transcripts involved in cellular processes important for the adaptation of bacteria to different growth conditions.

-	~~Authors: Gao~~, A., Vasilyev, N., Kaushik, A., Duan, W., Serganov, A.	+	Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.,Gao A, Vasilyev N, Kaushik A, Duan W, Serganov A Nucleic Acids Res. 2020 Jan 21. pii: 5710779. doi: 10.1093/nar/gkaa024. PMID:31960065<ref>PMID:31960065</ref>

-	~~Description: Crystal structure~~ of E.~~coli RppH in complex with GTP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6vcq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Duan, W]]		[[Category: Duan, W]]
-	[[Category: ~~Serganov~~, A]]	+	[[Category: Gao, A]]
	[[Category: Kaushik, A]]		[[Category: Kaushik, A]]
		+	[[Category: Serganov, A]]
	[[Category: Vasilyev, N]]		[[Category: Vasilyev, N]]
-	[[Category: ~~Gao, A~~]]	+	[[Category: Rna binding protein]]
		+	[[Category: Rna degradation]]

OCA at 14:18, 22 January 2020

OCA — Wed, 22 Jan 2020 14:18:21 GMT

←Older revision		Revision as of 14:18, 22 January 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Gao, A., Vasilyev, N., Kaushik, A., Duan, W., Serganov, A.		Authors: Gao, A., Vasilyev, N., Kaushik, A., Duan, W., Serganov, A.

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

OCA — Wed, 01 Jan 2020 06:51:15 GMT

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

←Older revision

Revision as of 06:51, 1 January 2020

OCA: New page: '''Unreleased structure''' The entry 6vcq is ON HOLD Authors: Gao, A., Vasilyev, N., Kaushik, A., Duan, W., Serganov, A. Description: Crystal structure of E.coli RppH in complex with G...

OCA — Wed, 01 Jan 2020 06:51:14 GMT

New page: '''Unreleased structure''' The entry 6vcq is ON HOLD Authors: Gao, A., Vasilyev, N., Kaushik, A., Duan, W., Serganov, A. Description: Crystal structure of E.coli RppH in complex with G...

New page

'''Unreleased structure'''

The entry 6vcq is ON HOLD

Authors: Gao, A., Vasilyev, N., Kaushik, A., Duan, W., Serganov, A.

Description: Crystal structure of E.coli RppH in complex with GTP
[[Category: Unreleased Structures]]
[[Category: Duan, W]]
[[Category: Serganov, A]]
[[Category: Kaushik, A]]
[[Category: Vasilyev, N]]
[[Category: Gao, A]]