7afq: Difference between revisions

Latest revision as of 11:10, 14 June 2023

Ribosome binding factor A (RbfA)

Structural highlights

7afq is a 1 chain structure with sequence from Escherichia coli O26:H11. This structure supersedes the now removed PDB entry 6r8d. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RBFA_ECOLI Essential for efficient processing of 16S rRNA. Probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. Could be some accessory protein needed for efficient assembly of the 30S subunit. May interact with the 5'-terminal helix region of 16S rRNA. Has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Overexpression suppresses a cold-sensitive C23U 16S rRNA mutation and rimM deletion mutants. Its function probably overlaps Era.^[1] ^[2]

Publication Abstract from PubMed

While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.

A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.,Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR Sci Adv. 2021 Jun 4;7(23). pii: 7/23/eabf7547. doi: 10.1126/sciadv.abf7547. Print, 2021 Jun. PMID:34088665^[3]

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

References

↑ Bylund GO, Wipemo LC, Lundberg LA, Wikstrom PM. RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli. J Bacteriol. 1998 Jan;180(1):73-82. PMID:9422595
↑ Inoue K, Chen J, Tan Q, Inouye M. Era and RbfA have overlapping function in ribosome biogenesis in Escherichia coli. J Mol Microbiol Biotechnol. 2006;11(1-2):41-52. PMID:16825789 doi:10.1159/000092818
↑ Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR. A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. Sci Adv. 2021 Jun 4;7(23). pii: 7/23/eabf7547. doi: 10.1126/sciadv.abf7547. Print, 2021 Jun. PMID:34088665 doi:https://dx.doi.org/10.1126/sciadv.abf7547

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OCA

[1] Bylund GO, Wipemo LC, Lundberg LA, Wikstrom PM. RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli. J Bacteriol. 1998 Jan;180(1):73-82. PMID:9422595

[2] Inoue K, Chen J, Tan Q, Inouye M. Era and RbfA have overlapping function in ribosome biogenesis in Escherichia coli. J Mol Microbiol Biotechnol. 2006;11(1-2):41-52. PMID:16825789 doi:10.1159/000092818

[3] Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR. A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. Sci Adv. 2021 Jun 4;7(23). pii: 7/23/eabf7547. doi: 10.1126/sciadv.abf7547. Print, 2021 Jun. PMID:34088665 doi:https://dx.doi.org/10.1126/sciadv.abf7547

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Ribosome binding factor A (RbfA)==
-<StructureSection load='7afq' size='340' side='right'caption='[[7afq]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='7afq' size='340' side='right'caption='[[7afq]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7afq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_o26:h11 Escherichia coli o26:h11]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6r8d 6r8d]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AFQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7afq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O26:H11 Escherichia coli O26:H11]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6r8d 6r8d]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AFQ FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rbfA, B9S25_002975 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=244319 Escherichia coli O26:H11])</td></tr>
+</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=7afq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7afq OCA], [https://pdbe.org/7afq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7afq RCSB], [https://www.ebi.ac.uk/pdbsum/7afq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7afq 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=7afq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7afq OCA], [https://pdbe.org/7afq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7afq RCSB], [https://www.ebi.ac.uk/pdbsum/7afq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7afq ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/A0A5B7PAU8_ECOLX A0A5B7PAU8_ECOLX]] One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.[HAMAP-Rule:MF_00003]
+[https://www.uniprot.org/uniprot/RBFA_ECOLI RBFA_ECOLI] Essential for efficient processing of 16S rRNA. Probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. Could be some accessory protein needed for efficient assembly of the 30S subunit. May interact with the 5'-terminal helix region of 16S rRNA. Has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Overexpression suppresses a cold-sensitive C23U 16S rRNA mutation and rimM deletion mutants. Its function probably overlaps Era.<ref>PMID:9422595</ref> <ref>PMID:16825789</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli o26:h11]]
+[[Category: Escherichia coli O26:H11]]
 [[Category: Large Structures]]
-[[Category: Connell, S]]
+[[Category: Connell S]]
-[[Category: Diercks, T]]
+[[Category: Diercks T]]
-[[Category: Fucini, P]]
+[[Category: Fucini P]]
-[[Category: Iturrioz, I]]
+[[Category: Iturrioz I]]
-[[Category: Ochoa-Lizarralde, B]]
+[[Category: Ochoa-Lizarralde B]]
-[[Category: Schedlbauer, A]]
+[[Category: Schedlbauer A]]
-[[Category: 30s biogenesis]]
-[[Category: Rbfa]]
-[[Category: Ribosome assembly]]
-[[Category: Rna binding protein]]
-[[Category: Solution state nmr]]

7afq: Difference between revisions

Latest revision as of 11:10, 14 June 2023

Ribosome binding factor A (RbfA)

Structural highlights

Function

Publication Abstract from PubMed

References

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