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3tv1

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Revision as of 15:13, 4 August 2016

Crystal structure of RtcA.AMP product complex

Structural highlights

3tv1 is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , ,
Related:	1qmh, 1qmi, 3kgd, 3tut, 3tux, 3tw3
Gene:	b4475, JW5688, rtcA, yhgJ, yhgK (ECOLI)
Activity:	RNA-3'-phosphate cyclase, with EC number 6.5.1.4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RTCA_ECOLI] Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.^[1]

Publication Abstract from PubMed

RNA 3'-phosphate cyclase (RtcA) synthesizes RNA 2',3' cyclic phosphate ends via three steps: reaction with ATP to form a covalent RtcA-(histidinyl-Nepsilon)-AMP intermediate; transfer of adenylate to an RNA 3'-phosphate to form RNA(3')pp(5')A; and attack of the vicinal O2' on the 3'-phosphorus to form a 2',3' cyclic phosphate and release AMP. Here we report the crystal structures of RtcA*ATP, RtcA*ATP*Mn(2+), and RtcA*ATP*Co(2+) substrate complexes and an RtcA*AMP product complex. Together with the structures of RtcA apoenzyme and the covalent RtcA-AMP intermediate, they illuminate the mechanism of nucleotidyl transfer, especially the stereochemical transitions at the AMP phosphate, the critical role of the metal in orienting the PP(i) leaving group of ATP during step 1, and the protein conformational switches that accompany substrate binding and product release. The octahedral metal complex of RtcA*ATP*Mn(2+) includes nonbridging oxygens from each of the ATP phosphates, two waters, and Glu14 as the sole RtcA component. Whereas the RtcA adenylylation step is metal-catalyzed, the subsequent steps in the cyclization pathway are metal-independent.

Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.,Chakravarty AK, Smith P, Shuman S Proc Natl Acad Sci U S A. 2011 Dec 13. PMID:22167800^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Genschik P, Drabikowski K, Filipowicz W. Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon. J Biol Chem. 1998 Sep 25;273(39):25516-26. PMID:9738023
↑ Chakravarty AK, Smith P, Shuman S. Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis. Proc Natl Acad Sci U S A. 2011 Dec 13. PMID:22167800 doi:10.1073/pnas.1115560108

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3tv1"

@@ Line 1: / Line 1: @@
 ==Crystal structure of RtcA.AMP product complex==
 <StructureSection load='3tv1' size='340' side='right' caption='[[3tv1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3tv1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3tv1]] is a 2 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=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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">[[1qmh|1qmh]], [[1qmi|1qmi]], [[3kgd|3kgd]], [[3tut|3tut]], [[3tux|3tux]], [[3tw3|3tw3]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b4475, JW5688, rtcA, yhgJ, yhgK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b4475, JW5688, rtcA, yhgJ, yhgK ([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/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [http://www.ebi.ac.uk/pdbsum/3tv1 PDBsum]</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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [http://pdbe.org/3tv1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [http://www.ebi.ac.uk/pdbsum/3tv1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tv1 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3tv1" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Ecoli]]
 [[Category: RNA-3'-phosphate cyclase]]
 [[Category: Chakravarty, A K]]

3tv1

From Proteopedia

Revision as of 15:13, 4 August 2016

Crystal structure of RtcA.AMP product complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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