8dcd - Revision history

OCA at 17:26, 18 October 2023

2023-10-18T17:26:51Z

← Older revision		Revision as of 17:26, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8dcd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCD FirstGlance]. <br>		<table><tr><td colspan='2'>[[8dcd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.22Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8dcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcd OCA], [https://pdbe.org/8dcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcd RCSB], [https://www.ebi.ac.uk/pdbsum/8dcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcd 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=8dcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcd OCA], [https://pdbe.org/8dcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcd RCSB], [https://www.ebi.ac.uk/pdbsum/8dcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcd ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:50, 9 November 2022

2022-11-09T07:50:38Z

← Older revision		Revision as of 07:50, 9 November 2022
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	~~'''Unreleased structure'''~~

	~~The entry~~ 8dcd is ~~ON HOLD until Paper~~ Publication		==RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and GTP==
			<StructureSection load='8dcd' size='340' side='right'caption='[[8dcd]], [[Resolution\|resolution]] 2.22Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[8dcd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCD FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8dcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcd OCA], [https://pdbe.org/8dcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcd RCSB], [https://www.ebi.ac.uk/pdbsum/8dcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcd ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Pyrococcus horikoshii (Pho) RtcB exemplifies a family of binuclear transition metal- and GTP-dependent RNA ligases that join 3'-phosphate and 5'-OH ends via RtcB-(histidinyl-N)-GMP and RNA3'pp5'G intermediates. We find that guanylylation of PhoRtcB is optimal with manganese and less effective with cobalt and nickel. Zinc and copper are inactive and potently inhibit manganese-dependent guanylylation. We report crystal structures of PhoRtcB in complexes with GTP and permissive (Mn, Co, Ni) or inhibitory (Zn, Cu) metals. Zinc and copper occupy the M1 and M2 sites adjacent to the GTP phosphates, as do manganese, cobalt, and nickel. The identity/positions of enzymic ligands for M1 (His234, His329, Cys98) and M2 (Cys98, Asp95, His203) are the same for permissive and inhibitory metals. The differences pertain to: (i) the coordination geometries and phosphate contacts of the metals; and (ii) the orientation of the His404 nucleophile with respect to the GTP alpha-phosphate and pyrophosphate leaving group. M2 metal coordination geometry correlates with metal cofactor activity, whereby inhibitory Zn2 and Cu2 assume a tetrahedral configuration and contact only the GTP gamma-phosphate, whereas Mn2, Co2, and Ni2 coordination complexes are pentahedral and contact the beta- and gamma-phosphates. The His404-Nepsilon-Palpha-O(alpha-beta) angle is closer to apical in Mn (179 degrees ), Co (171 degrees ), and Ni (169 degrees ) structures than in Zn (160 degrees ) and Cu (155 degrees ) structures. The octahedral Mn1 geometry in our RtcBGTPMn(2+) structure, in which Mn1 contacts alpha-, beta-, and gamma-phosphates, transitions to a tetrahedral configuration after formation of RtcB(His404)-GMPMn(2+) and departure of pyrophosphate.

	~~Authors:~~ Jacewicz, A., Dantuluri, S., Shuman, S.		Structures of RNA ligase RtcB in complexes with divalent cations and GTP.,Jacewicz A, Dantuluri S, Shuman S RNA. 2022 Nov;28(11):1509-1518. doi: 10.1261/rna.079327.122. Epub 2022 Sep 1. PMID:36130078<ref>PMID:36130078</ref>

	~~Description~~: ~~RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and GTP~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: Dantuluri, S]]		<div class="pdbe-citations 8dcd" style="background-color:#fffaf0;"></div>
	[[Category: Jacewicz, A]]		== References ==
	[[Category: Shuman, S]]		<references/>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Pyrococcus horikoshii OT3]]
			[[Category: Dantuluri S]]
			[[Category: Jacewicz A]]
			[[Category: Shuman S]]

OCA at 15:11, 6 July 2022

2022-07-06T15:11:27Z

← Older revision		Revision as of 15:11, 6 July 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8dcd is ON HOLD		The entry 8dcd is ON HOLD until Paper Publication

	Authors: Jacewicz, A., Dantuluri, S., Shuman, S.		Authors: Jacewicz, A., Dantuluri, S., Shuman, S.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Dantuluri, S]]		[[Category: Dantuluri, S]]
			[[Category: Jacewicz, A]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
	~~[[Category: Jacewicz, A]]~~

OCA: Protected "8dcd" [edit=sysop:move=sysop]

2022-06-22T07:30:57Z

Protected "8dcd" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:30, 22 June 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8dcd is ON HOLD Authors: Jacewicz, A., Dantuluri, S., Shuman, S. Description: RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and G...

2022-06-22T07:30:56Z

New page: '''Unreleased structure''' The entry 8dcd is ON HOLD Authors: Jacewicz, A., Dantuluri, S., Shuman, S. Description: RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and G...

New page

'''Unreleased structure'''

The entry 8dcd is ON HOLD

Authors: Jacewicz, A., Dantuluri, S., Shuman, S.

Description: RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and GTP
[[Category: Unreleased Structures]]
[[Category: Dantuluri, S]]
[[Category: Shuman, S]]
[[Category: Jacewicz, A]]