3kgd

From Proteopedia

(Difference between revisions)

Revision as of 23:02, 4 August 2016

Crystal structure of E. coli RNA 3' cyclase

Structural highlights

3kgd is a 4 chain structure with sequence from Escherichia coli mg1655. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Gene:	b4475, JW5688, rtcA, yhgJ, yhgK, YP_026219 (Escherichia coli MG1655)
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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-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. Here we report the 1.7 A crystal structure of the RtcA-AMP intermediate, which reveals the mechanism of nucleotidyl transfer. Adenylate is linked via a phosphoamide bond to the His309 Nepsilon atom. A network of hydrogen bonds to the ribose O2' and O3' accounts for the stringent ribonucleotide preference. Adenine is sandwiched in a hydrophobic pocket between Tyr284 and Pro131 and the preference for adenine is enforced by Phe135, which packs against the purine C2 edge. Two sulfates bound near the adenylate plausibly mimic the 3'-terminal and penultimate phosphates of RNA. The structure illuminates how the four alpha2/beta4 domains contribute to substrate binding and catalysis.

Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer.,Tanaka N, Smith P, Shuman S Structure. 2010 Mar 14;18(4):449-57. PMID:20399182^[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
↑ Tanaka N, Smith P, Shuman S. Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer. Structure. 2010 Mar 14;18(4):449-57. PMID:20399182 doi:10.1016/j.str.2010.01.016

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of E. coli RNA 3' cyclase==
 <StructureSection load='3kgd' size='340' side='right' caption='[[3kgd]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kgd]] is a 4 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=3KGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KGD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kgd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_mg1655 Escherichia coli mg1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KGD 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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">b4475, JW5688, rtcA, yhgJ, yhgK, YP_026219 ([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, YP_026219 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511145 Escherichia coli MG1655])</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=3kgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kgd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kgd RCSB], [http://www.ebi.ac.uk/pdbsum/3kgd 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=3kgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kgd OCA], [http://pdbe.org/3kgd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kgd RCSB], [http://www.ebi.ac.uk/pdbsum/3kgd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kgd ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kgd ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3kgd" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Escherichia coli mg1655]]
 [[Category: RNA-3'-phosphate cyclase]]
 [[Category: Shuman, S]]

3kgd

From Proteopedia

Revision as of 23:02, 4 August 2016

Crystal structure of E. coli RNA 3' cyclase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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