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1yt3

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Revision as of 08:52, 20 January 2021

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

Structural highlights

1yt3 is a 1 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	RND ("Bacillus coli" Migula 1895)
Activity:	Ribonuclease III, with EC number 3.1.26.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RND_ECOLI] Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.^[1] ^[2]

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

RNase D (RND) is one of seven exoribonucleases identified in Escherichia coli. RNase D has homologs in many eubacteria and eukaryotes, and has been shown to contribute to the 3' maturation of several stable RNAs. Here, we report the 1.6 A resolution crystal structure of E. coli RNase D. The conserved DEDD residues of RNase D fold into an arrangement very similar to the Klenow fragment exonuclease domain. Besides the catalytic domain, RNase D also contains two structurally similar alpha-helical domains with no discernible sequence homology between them. These closely resemble the HRDC domain previously seen in RecQ-family helicases and several other proteins acting on nucleic acids. More interestingly, the DEDD catalytic domain and the two helical domains come together to form a ring-shaped structure. The ring-shaped architecture of E. coli RNase D and the HRDC domains likely play a major role in determining the substrate specificity of this exoribonuclease.

Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing.,Zuo Y, Wang Y, Malhotra A Structure. 2005 Jul;13(7):973-84. PMID:16004870^[3]

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

References

↑ Zhang JR, Deutscher MP. Escherichia coli RNase D: sequencing of the rnd structural gene and purification of the overexpressed protein. Nucleic Acids Res. 1988 Jul 25;16(14A):6265-78. PMID:3041371
↑ Cudny H, Zaniewski R, Deutscher MP. Escherichia coli RNase D. Catalytic properties and substrate specificity. J Biol Chem. 1981 Jun 10;256(11):5633-7. PMID:6263886
↑ Zuo Y, Wang Y, Malhotra A. Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing. Structure. 2005 Jul;13(7):973-84. PMID:16004870 doi:10.1016/j.str.2005.04.015

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yt3"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing==
-<StructureSection load='1yt3' size='340' side='right' caption='[[1yt3]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='1yt3' size='340' side='right'caption='[[1yt3]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://pdbe.org/1yt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://pdbe.org/1yt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 *[[Temp|Temp]]
 == References ==
@@ Line 39: / Line 39: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: Ribonuclease III]]
 [[Category: Malhotra, A]]

1yt3

From Proteopedia

Revision as of 08:52, 20 January 2021

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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