3gib

From Proteopedia

(Difference between revisions)

Revision as of 21:52, 8 February 2016

Crystal Stucture of the Complex of the E. coli Hfq with Poly(A)

Structural highlights

3gib is a 4 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	b4172, hfq, JW4130 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[HFQ_ECOLI] RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Involved in the regulation of stress responses mediated by the sigma factors RpoS, sigma-E and sigma-32. Binds with high specificity to tRNAs. In vitro, stimulates synthesis of long tails by poly(A) polymerase I. Required for RNA phage Qbeta replication.^[1] ^[2] ^[3] ^[4] ^[5] Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation.^[6] ^[7] ^[8] ^[9] ^[10]

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

Hfq is a small, highly abundant hexameric protein that is found in many bacteria and plays a critical role in mRNA expression and RNA stability. As an "RNA chaperone," Hfq binds AU-rich sequences and facilitates the trans annealing of small RNAs (sRNAs) to their target mRNAs, typically resulting in the down-regulation of gene expression. Hfq also plays a key role in bacterial RNA decay by binding tightly to polyadenylate [poly(A)] tracts. The structural mechanism by which Hfq recognizes and binds poly(A) is unknown. Here, we report the crystal structure of Escherichia coli Hfq bound to the poly(A) RNA, A(15). The structure reveals a unique RNA binding mechanism. Unlike uridine-containing sequences, which bind to the "proximal" face, the poly(A) tract binds to the "distal" face of Hfq using 6 tripartite binding motifs. Each motif consists of an adenosine specificity site (A site), which is effected by peptide backbone hydrogen bonds, a purine nucleotide selectivity site (R site), and a sequence-nondiscriminating RNA entrance/exit site (E site). The resulting implication that Hfq can bind poly(A-R-N) triplets, where R is a purine nucleotide and N is any nucleotide, was confirmed by binding studies. Indeed, Hfq bound to the oligoribonucleotides (AGG)(8), (AGC)(8), and the shorter (A-R-N)(4) sequence, AACAACAAGAAG, with nanomolar affinities. The abundance of (A-R-N)(4) and (A-R-N)(5) triplet repeats in the E. coli genome suggests additional RNA targets for Hfq. Further, the structure provides insight into Hfq-mediated sRNA-mRNA annealing and the role of Hfq in RNA decay.

Structure of Escherichia coli Hfq bound to polyriboadenylate RNA.,Link TM, Valentin-Hansen P, Brennan RG Proc Natl Acad Sci U S A. 2009 Nov 4. PMID:19889981^[11]

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

References

↑ Carmichael GG, Weber K, Niveleau A, Wahba AJ. The host factor required for RNA phage Qbeta RNA replication in vitro. Intracellular location, quantitation, and purification by polyadenylate-cellulose chromatography. J Biol Chem. 1975 May 25;250(10):3607-612. PMID:805130
↑ Hajnsdorf E, Regnier P. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1501-5. PMID:10677490 doi:10.1073/pnas.040549897
↑ Sledjeski DD, Whitman C, Zhang A. Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol. 2001 Mar;183(6):1997-2005. PMID:11222598 doi:10.1128/JB.183.6.1997-2005.2001
↑ Guisbert E, Rhodius VA, Ahuja N, Witkin E, Gross CA. Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli. J Bacteriol. 2007 Mar;189(5):1963-73. Epub 2006 Dec 8. PMID:17158661 doi:10.1128/JB.01243-06
↑ Kim Y, Wood TK. Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem Biophys Res Commun. 2010 Jan 1;391(1):209-13. doi:, 10.1016/j.bbrc.2009.11.033. Epub 2009 Nov 10. PMID:19909729 doi:10.1016/j.bbrc.2009.11.033
↑ Carmichael GG, Weber K, Niveleau A, Wahba AJ. The host factor required for RNA phage Qbeta RNA replication in vitro. Intracellular location, quantitation, and purification by polyadenylate-cellulose chromatography. J Biol Chem. 1975 May 25;250(10):3607-612. PMID:805130
↑ Hajnsdorf E, Regnier P. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1501-5. PMID:10677490 doi:10.1073/pnas.040549897
↑ Sledjeski DD, Whitman C, Zhang A. Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol. 2001 Mar;183(6):1997-2005. PMID:11222598 doi:10.1128/JB.183.6.1997-2005.2001
↑ Guisbert E, Rhodius VA, Ahuja N, Witkin E, Gross CA. Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli. J Bacteriol. 2007 Mar;189(5):1963-73. Epub 2006 Dec 8. PMID:17158661 doi:10.1128/JB.01243-06
↑ Kim Y, Wood TK. Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem Biophys Res Commun. 2010 Jan 1;391(1):209-13. doi:, 10.1016/j.bbrc.2009.11.033. Epub 2009 Nov 10. PMID:19909729 doi:10.1016/j.bbrc.2009.11.033
↑ Link TM, Valentin-Hansen P, Brennan RG. Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. Proc Natl Acad Sci U S A. 2009 Nov 4. PMID:19889981

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/3gib"

@@ Line 2: / Line 2: @@
 <StructureSection load='3gib' size='340' side='right' caption='[[3gib]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gib]] 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=3GIB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GIB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gib]] is a 4 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=3GIB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GIB FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b4172, hfq, JW4130 ([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">b4172, hfq, JW4130 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3gib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gib OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gib RCSB], [http://www.ebi.ac.uk/pdbsum/3gib 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=3gib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gib OCA], [http://pdbe.org/3gib PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gib RCSB], [http://www.ebi.ac.uk/pdbsum/3gib PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 17: @@
     <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=3gib ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3gib" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Ecoli]]
 [[Category: Brennan, R G]]
 [[Category: Link, T M]]

3gib

From Proteopedia

Revision as of 21:52, 8 February 2016

Crystal Stucture of the Complex of the E. coli Hfq with Poly(A)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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