5izo

From Proteopedia

(Difference between revisions)

Revision as of 07:19, 6 October 2017

Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site

Structural highlights

5izo is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	5ipp, 5iuf, 5j2z
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NRNA_BACSU] Bifunctional enzyme which has both oligoribonuclease and pAp-phosphatase activities. Degrades RNA and DNA oligonucleotides with a length of 5 nucleotides and shorter, with a preference for 3-mers. Directionality is controversial; shown to degrade 5-mers and less in a 3' to 5' direction (PubMed:17586819), and 11-mers in a 5' to 3' direction (PubMed:21087930). Converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The final step in RNA degradation is the hydrolysis of RNA fragments five nucleotides or less in length (nanoRNA) to mononucleotides. In Escherichia coli this step is carried out by oligoribonuclease (Orn), a DEDD-family exoribonuclease that is conserved throughout eukaryotes. However, many bacteria lack Orn homologs, and an unrelated DHH-family phosphoesterase, NrnA, has recently been identified as one of the enzymes responsible for nanoRNA degradation in Bacillus subtilis. To understand its mechanism of action, B. subtilis NrnA was purified and crystallized at room temperature using the hanging-drop vapor-diffusion method with PEG 4000, PEG 3350 or PEG MME 2000 as precipitant. The crystals belonged to the primitive monoclinic space group P2(1), with unit-cell parameters a = 50.62, b = 121.3, c = 123.4 A, alpha = 90, beta = 91.31, gamma = 90 degrees .

Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation.,Nelersa CM, Schmier BJ, Malhotra A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Oct 1;67(Pt 10):1235-8., doi: 10.1107/S1744309111026509. Epub 2011 Sep 29. PMID:22102036^[4]

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

References

↑ Mechold U, Fang G, Ngo S, Ogryzko V, Danchin A. YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity. Nucleic Acids Res. 2007;35(13):4552-61. Epub 2007 Jun 22. PMID:17586819 doi:http://dx.doi.org/10.1093/nar/gkm462
↑ Wakamatsu T, Kim K, Uemura Y, Nakagawa N, Kuramitsu S, Masui R. Role of RecJ-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation. J Biol Chem. 2011 Jan 28;286(4):2807-16. doi: 10.1074/jbc.M110.161596. Epub 2010 , Nov 18. PMID:21087930 doi:http://dx.doi.org/10.1074/jbc.M110.161596
↑ Postic G, Danchin A, Mechold U. Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae. RNA. 2012 Jan;18(1):155-65. doi: 10.1261/rna.029132.111. Epub 2011 Nov 23. PMID:22114320 doi:http://dx.doi.org/10.1261/rna.029132.111
↑ Nelersa CM, Schmier BJ, Malhotra A. Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Oct 1;67(Pt 10):1235-8., doi: 10.1107/S1744309111026509. Epub 2011 Sep 29. PMID:22102036 doi:http://dx.doi.org/10.1107/S1744309111026509

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5izo"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5izo is ON HOLD  until Paper Publication
+==Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site==
+<StructureSection load='5izo' size='340' side='right' caption='[[5izo]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IZO FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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">[[5ipp|5ipp]], [[5iuf|5iuf]], [[5j2z|5j2z]]</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=5izo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5izo OCA], [http://pdbe.org/5izo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5izo RCSB], [http://www.ebi.ac.uk/pdbsum/5izo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5izo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/NRNA_BACSU NRNA_BACSU]] Bifunctional enzyme which has both oligoribonuclease and pAp-phosphatase activities. Degrades RNA and DNA oligonucleotides with a length of 5 nucleotides and shorter, with a preference for 3-mers. Directionality is controversial; shown to degrade 5-mers and less in a 3' to 5' direction (PubMed:17586819), and 11-mers in a 5' to 3' direction (PubMed:21087930). Converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP.<ref>PMID:17586819</ref> <ref>PMID:21087930</ref> <ref>PMID:22114320</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The final step in RNA degradation is the hydrolysis of RNA fragments five nucleotides or less in length (nanoRNA) to mononucleotides. In Escherichia coli this step is carried out by oligoribonuclease (Orn), a DEDD-family exoribonuclease that is conserved throughout eukaryotes. However, many bacteria lack Orn homologs, and an unrelated DHH-family phosphoesterase, NrnA, has recently been identified as one of the enzymes responsible for nanoRNA degradation in Bacillus subtilis. To understand its mechanism of action, B. subtilis NrnA was purified and crystallized at room temperature using the hanging-drop vapor-diffusion method with PEG 4000, PEG 3350 or PEG MME 2000 as precipitant. The crystals belonged to the primitive monoclinic space group P2(1), with unit-cell parameters a = 50.62, b = 121.3, c = 123.4 A, alpha = 90, beta = 91.31, gamma = 90 degrees .
-Authors: Schmier, B.J., Malhotra, A., Nelersa, C.M.
+Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation.,Nelersa CM, Schmier BJ, Malhotra A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Oct 1;67(Pt 10):1235-8., doi: 10.1107/S1744309111026509. Epub 2011 Sep 29. PMID:22102036<ref>PMID:22102036</ref>
-Description: Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5izo" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribonuclease|Ribonuclease]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Malhotra, A]]
-[[Category: Schmier, B.J]]
+[[Category: Nelersa, C M]]
-[[Category: Nelersa, C.M]]
+[[Category: Schmier, B J]]
+[[Category: Abortive transcript]]
+[[Category: B. subtili]]
+[[Category: Exonuclease]]
+[[Category: Hydrolase]]
+[[Category: Nanorna]]
+[[Category: Pap phosphatase]]
+[[Category: Rna degradation]]
+[[Category: Rnase]]

5izo

From Proteopedia

Revision as of 07:19, 6 October 2017

Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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