7oqx - Revision history

OCA at 12:54, 1 February 2024

OCA — Thu, 01 Feb 2024 12:54:51 GMT

←Older revision		Revision as of 12:54, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7oqx' size='340' side='right'caption='[[7oqx]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='7oqx' size='340' side='right'caption='[[7oqx]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7oqx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7oqx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Planococcus_halocryophilus Planococcus halocryophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OQX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6qxn\|6qxn]], [[6qy6\|6qy6]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=7oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oqx OCA], [https://pdbe.org/7oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oqx RCSB], [https://www.ebi.ac.uk/pdbsum/7oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oqx ProSAT]</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=7oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oqx OCA], [https://pdbe.org/7oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oqx RCSB], [https://www.ebi.ac.uk/pdbsum/7oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oqx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A1C7DQ98_9BACL A0A1C7DQ98_9BACL]] Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate.[SAAS:SAAS00711016]	+	[https://www.uniprot.org/uniprot/A0A1C7DQ98_9BACL A0A1C7DQ98_9BACL] Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate.[SAAS:SAAS00711016]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7oqx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7oqx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[CCA-adding enzyme 3D structures\|CCA-adding enzyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Betat, H]]	+	[[Category: Planococcus halocryophilus]]
-	[[Category: Bluhm, A]]	+	[[Category: Betat H]]
-	[[Category: Hennig, O]]	+	[[Category: Bluhm A]]
-	[[Category: Lorber, B]]	+	[[Category: Hennig O]]
-	[[Category: Moerl, M]]	+	[[Category: Lorber B]]
-	[[Category: Rollet, K]]	+	[[Category: Moerl M]]
-	[[Category: Sauter, C]]	+	[[Category: Rollet K]]
-	[[Category: Wijn, R ~~de]]~~	+	[[Category: Sauter C]]
-	~~[[Category: Psychrophilic enzyme]]~~	+	[[Category: De Wijn R]]
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Trna maturation]]~~	+
-	~~[[Category: Trna nucleotidyltransferase~~]]	+

OCA at 12:49, 24 November 2021

OCA — Wed, 24 Nov 2021 12:49:37 GMT

←Older revision		Revision as of 12:49, 24 November 2021
Line 1:		Line 1:

	==Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP==		==Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP==
-	<StructureSection load='7oqx' size='340' side='right'caption='[[7oqx]]' scene=''>	+	<StructureSection load='7oqx' size='340' side='right'caption='[[7oqx]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7oqx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OQX FirstGlance]. <br>
-	</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=7oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oqx OCA], [https://pdbe.org/7oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oqx RCSB], [https://www.ebi.ac.uk/pdbsum/7oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oqx ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6qxn\|6qxn]], [[6qy6\|6qy6]]</div></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=7oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oqx OCA], [https://pdbe.org/7oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oqx RCSB], [https://www.ebi.ac.uk/pdbsum/7oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oqx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A1C7DQ98_9BACL A0A1C7DQ98_9BACL]] Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate.[SAAS:SAAS00711016]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CCA-adding enzymes are highly specific RNA polymerases that add and maintain the sequence C-C-A at tRNA 3'-ends. Recently, we could reveal that cold adaptation of such a polymerase is not only achieved at the expense of enzyme stability, but also at the cost of polymerization fidelity. Enzymes from psychrophilic organisms usually show an increased structural flexibility to enable catalysis at low temperatures. Here, polymerases face a dilemma, as there is a discrepancy between the need for a tightly controlled flexibility during polymerization and an increased flexibility as strategy for cold adaptation. Based on structural and biochemical analyses, we contribute to clarify the cold adaptation strategy of the psychrophilic CCA-adding enzyme from Planococcus halocryophilus, a gram-positive bacterium thriving in the arctic permafrost at low temperatures down to -15 degrees C. A comparison with the closely related enzyme from the thermophilic bacterium Geobacillus stearothermophilus reveals several features of cold adaptation - a significantly reduced amount of alpha-helical elements in the C-terminal tRNA-binding region and a structural adaptation in one of the highly conserved catalytic core motifs located in the N-terminal catalytic core of the enzyme.
		+
		+	CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus.,de Wijn R, Rollet K, Ernst FGM, Wellner K, Betat H, Morl M, Sauter C Comput Struct Biotechnol J. 2021 Oct 21;19:5845-5855. doi:, 10.1016/j.csbj.2021.10.018. eCollection 2021. PMID:34765099<ref>PMID:34765099</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7oqx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Betat H]]	+	[[Category: Betat, H]]
-	[[Category: Bluhm A]]	+	[[Category: Bluhm, A]]
-	[[Category: Hennig O]]	+	[[Category: Hennig, O]]
-	[[Category: Lorber B]]	+	[[Category: Lorber, B]]
-	[[Category: Moerl M]]	+	[[Category: Moerl, M]]
-	[[Category: Rollet K]]	+	[[Category: Rollet, K]]
-	[[Category: Sauter C]]	+	[[Category: Sauter, C]]
-	[[Category: De Wijn R]]	+	[[Category: Wijn, R de]]
		+	[[Category: Psychrophilic enzyme]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Trna maturation]]
		+	[[Category: Trna nucleotidyltransferase]]

OCA at 14:31, 3 November 2021

OCA — Wed, 03 Nov 2021 14:31:50 GMT

←Older revision		Revision as of 14:31, 3 November 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7oqx ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP==
-		+	<StructureSection load='7oqx' size='340' side='right'caption='[[7oqx]]' scene=''>
-	~~Authors~~: ~~Rollet, K~~.~~, de Wijn, R~~.~~, Bluhm, A~~.~~, Hennig, O~~., ~~Betat, H~~., ~~Moerl, M~~., ~~Lorber~~, B., ~~Sauter, C~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OQX FirstGlance]. <br>
-	~~Description: Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP~~	+	</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=7oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oqx OCA], [https://pdbe.org/7oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oqx RCSB], [https://www.ebi.ac.uk/pdbsum/7oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oqx ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Moerl, M~~]]	+	__TOC__
-	[[Category: ~~Lorber, B~~]]	+	</StructureSection>
-	[[Category: ~~De Wijn, R~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bluhm, A~~]]	+	[[Category: Betat H]]
-	[[Category: ~~Hennig, O~~]]	+	[[Category: Bluhm A]]
-	[[Category: Rollet, K]]	+	[[Category: Hennig O]]
-	[[Category: Sauter, C]]	+	[[Category: Lorber B]]
-	[[Category: ~~Betat, H~~]]	+	[[Category: Moerl M]]
		+	[[Category: Rollet K]]
		+	[[Category: Sauter C]]
		+	[[Category: De Wijn R]]

OCA at 08:48, 7 July 2021

OCA — Wed, 07 Jul 2021 08:48:56 GMT

←Older revision		Revision as of 08:48, 7 July 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7oqx is ON HOLD	+	The entry 7oqx is ON HOLD until Paper Publication

	Authors: Rollet, K., de Wijn, R., Bluhm, A., Hennig, O., Betat, H., Moerl, M., Lorber, B., Sauter, C.		Authors: Rollet, K., de Wijn, R., Bluhm, A., Hennig, O., Betat, H., Moerl, M., Lorber, B., Sauter, C.
Line 7:		Line 7:
	Description: Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP		Description: Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Bluhm, A]]
	[[Category: Moerl, M]]		[[Category: Moerl, M]]
-	[[Category: Sauter, C]]
	[[Category: Lorber, B]]		[[Category: Lorber, B]]
-	[[Category: ~~Betat~~, H]]	+	[[Category: De Wijn, R]]
		+	[[Category: Bluhm, A]]
	[[Category: Hennig, O]]		[[Category: Hennig, O]]
	[[Category: Rollet, K]]		[[Category: Rollet, K]]
-	[[Category: ~~De Wijn~~, R]]	+	[[Category: Sauter, C]]
		+	[[Category: Betat, H]]

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

OCA — Thu, 17 Jun 2021 13:49:12 GMT

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

←Older revision

Revision as of 13:49, 17 June 2021

OCA: New page: '''Unreleased structure''' The entry 7oqx is ON HOLD Authors: Rollet, K., de Wijn, R., Bluhm, A., Hennig, O., Betat, H., Moerl, M., Lorber, B., Sauter, C. Description: Crystal structur...

OCA — Thu, 17 Jun 2021 13:49:11 GMT

New page: '''Unreleased structure''' The entry 7oqx is ON HOLD Authors: Rollet, K., de Wijn, R., Bluhm, A., Hennig, O., Betat, H., Moerl, M., Lorber, B., Sauter, C. Description: Crystal structur...

New page

'''Unreleased structure'''

The entry 7oqx is ON HOLD

Authors: Rollet, K., de Wijn, R., Bluhm, A., Hennig, O., Betat, H., Moerl, M., Lorber, B., Sauter, C.

Description: Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP
[[Category: Unreleased Structures]]
[[Category: Bluhm, A]]
[[Category: Moerl, M]]
[[Category: Sauter, C]]
[[Category: Lorber, B]]
[[Category: Betat, H]]
[[Category: Hennig, O]]
[[Category: Rollet, K]]
[[Category: De Wijn, R]]