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3moj

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Revision as of 11:51, 5 August 2016

Structure of the RNA binding domain of the Bacillus subtilis YxiN protein complexed with a fragment of 23S ribosomal RNA

Structural highlights

3moj is a 2 chain structure with sequence from [1] and "bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	dbpA, deaD, yxiN, BSU39110, SS8E ("Bacillus globigii" Migula 1900)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DBPA_BACSU] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes (Probable).^[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

DEAD-box RNA helicases of the bacterial DbpA subfamily are localized to their biological substrate when a carboxy-terminal RNA recognition motif domain binds tightly and specifically to a segment of 23S ribosomal RNA (rRNA) that includes hairpin 92 of the peptidyl transferase center. A complex between a fragment of 23S rRNA and the RNA binding domain (RBD) of the Bacillus subtilis DbpA protein YxiN was crystallized and its structure was determined to 2.9 A resolution, revealing an RNA recognition mode that differs from those observed with other RNA recognition motifs. The RBD is bound between two RNA strands at a three-way junction. Multiple phosphates of the RNA backbone interact with an electropositive band generated by lysines of the RBD. Nucleotides of the single-stranded loop of hairpin 92 interact with the RBD, including the guanosine base of G2553, which forms three hydrogen bonds with the peptide backbone. A G2553U mutation reduces the RNA binding affinity by 2 orders of magnitude, confirming that G2553 is a sequence specificity determinant in RNA binding. Binding of the RBD to 23S rRNA in the late stages of ribosome subunit maturation would position the ATP-binding duplex destabilization fragment of the protein for interaction with rRNA in the peptidyl transferase cleft of the subunit, allowing it to "melt out" unstable secondary structures and allow proper folding.

Structure of the RNA Binding Domain of a DEAD-Box Helicase Bound to Its Ribosomal RNA Target Reveals a Novel Mode of Recognition by an RNA Recognition Motif.,Hardin JW, Hu YX, McKay DB J Mol Biol. 2010 Jul 29. PMID:20673833^[3]

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

References

↑ Kossen K, Uhlenbeck OC. Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Nucleic Acids Res. 1999 Oct 1;27(19):3811-20. PMID:10481020
↑ Karow AR, Klostermeier D. A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN. Nucleic Acids Res. 2009 Jul;37(13):4464-71. doi: 10.1093/nar/gkp397. Epub 2009, May 27. PMID:19474341 doi:http://dx.doi.org/10.1093/nar/gkp397
↑ Hardin JW, Hu YX, McKay DB. Structure of the RNA Binding Domain of a DEAD-Box Helicase Bound to Its Ribosomal RNA Target Reveals a Novel Mode of Recognition by an RNA Recognition Motif. J Mol Biol. 2010 Jul 29. PMID:20673833 doi:10.1016/j.jmb.2010.07.040

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/3moj"

@@ Line 1: / Line 1: @@
 ==Structure of the RNA binding domain of the Bacillus subtilis YxiN protein complexed with a fragment of 23S ribosomal RNA==
 <StructureSection load='3moj' size='340' side='right' caption='[[3moj]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3moj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MOJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3moj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [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=3MOJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MOJ FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbpA, deaD, yxiN, BSU39110, SS8E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbpA, deaD, yxiN, BSU39110, SS8E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=3moj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3moj RCSB], [http://www.ebi.ac.uk/pdbsum/3moj 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=3moj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moj OCA], [http://pdbe.org/3moj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3moj RCSB], [http://www.ebi.ac.uk/pdbsum/3moj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3moj ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 16: / 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=3moj ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3moj" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 33: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus subtilis]]
+[[Category: Bacillus globigii migula 1900]]
-[[Category: Escherichia coli]]
 [[Category: Hardin, J W]]
 [[Category: Hu, Y]]

3moj

From Proteopedia

Revision as of 11:51, 5 August 2016

Structure of the RNA binding domain of the Bacillus subtilis YxiN protein complexed with a fragment of 23S ribosomal RNA

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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