3hsb

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer

Structural highlights

3hsb is a 7 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HFQ_BACSU 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. Also binds with high specificity to tRNAs.[HAMAP-Rule:MF_00436]

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

Bacterial Hfq is a protein that plays an important role in the regulation of genes in cooperation with sRNAs. Escherichia coli Hfq (EcHfq) has two or more sites that bind RNA(s) including U-rich and/or the poly(A) tail of mRNA. However, functional and structural information about Bacillus subtilis Hfq (BsHfq) including the RNA sequences that specifically bind to it remain unknown. Here, we describe RNA aptamers including fragment (AG)(3)A that are recognized by BsHfq and crystal structures of the BsHfq-(AG)(3)A complex at 2.2 A resolution. Mutational and structural studies revealed that the RNA fragment binds to the distal site, one of the two binding sites on Hfq, and identified amino acid residues that are critical for sequence-specific interactions between BsHfq and (AG)(3)A. In particular, R32 appears to interact with G bases in (AG)(3)A. Poly(A) also binds to the distal site of EcHfq, but the overall RNA structure and protein-RNA interaction patterns engaged in the R32 residues of BsHfq-(AG)(3)A differ from those of EcHfq-poly(A). These findings provide novel insight into how the Hfq homologue recognizes RNA.

Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq.,Someya T, Baba S, Fujimoto M, Kawai G, Kumasaka T, Nakamura K Nucleic Acids Res. 2012 Feb;40(4):1856-67. Epub 2011 Nov 3. PMID:22053080^[1]

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

References

↑ Someya T, Baba S, Fujimoto M, Kawai G, Kumasaka T, Nakamura K. Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq. Nucleic Acids Res. 2012 Feb;40(4):1856-67. Epub 2011 Nov 3. PMID:22053080 doi:http://dx.doi.org/10.1093/nar/gkr892

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/3hsb"

@@ Line 1: / Line 1: @@
 ==Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer==
-<StructureSection load='3hsb' size='340' side='right' caption='[[3hsb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='3hsb' size='340' side='right'caption='[[3hsb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hsb]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HSB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HSB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hsb]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HSB FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ymaH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</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=3hsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hsb OCA], [http://pdbe.org/3hsb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hsb RCSB], [http://www.ebi.ac.uk/pdbsum/3hsb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hsb ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hsb OCA], [https://pdbe.org/3hsb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hsb RCSB], [https://www.ebi.ac.uk/pdbsum/3hsb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hsb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HFQ_BACSU HFQ_BACSU]] 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. Also binds with high specificity to tRNAs.[HAMAP-Rule:MF_00436]
+[https://www.uniprot.org/uniprot/HFQ_BACSU HFQ_BACSU] 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. Also binds with high specificity to tRNAs.[HAMAP-Rule:MF_00436]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hs/3hsb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hs/3hsb_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 28: @@
 </div>
 <div class="pdbe-citations 3hsb" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Protein Hfq 3D structures|Protein Hfq 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus globigii migula 1900]]
+[[Category: Bacillus subtilis]]
-[[Category: Baba, S]]
+[[Category: Large Structures]]
-[[Category: Kawai, G]]
+[[Category: Baba S]]
-[[Category: Kumasaka, T]]
+[[Category: Kawai G]]
-[[Category: Nakamura, K]]
+[[Category: Kumasaka T]]
-[[Category: Someya, T]]
+[[Category: Nakamura K]]
-[[Category: Protein-rna complex]]
+[[Category: Someya T]]
-[[Category: Rna binding protein-rna complex]]
-[[Category: Rna-binding]]
-[[Category: Sm-like motif]]
-[[Category: Stress response]]

3hsb

From Proteopedia

Current revision

Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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