3r9w

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==Crystal structure of Era in complex with MgGDPNP and nucleotides 1506-1542 of 16S ribosomal RNA==
==Crystal structure of Era in complex with MgGDPNP and nucleotides 1506-1542 of 16S ribosomal RNA==
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<StructureSection load='3r9w' size='340' side='right' caption='[[3r9w]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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<StructureSection load='3r9w' size='340' side='right'caption='[[3r9w]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3r9w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R9W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R9W FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3r9w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R9W FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ega|1ega]], [[3ieu|3ieu]], [[3iev|3iev]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_1994, era, era1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r9w OCA], [https://pdbe.org/3r9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r9w RCSB], [https://www.ebi.ac.uk/pdbsum/3r9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r9w ProSAT]</span></td></tr>
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<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=3r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r9w OCA], [http://pdbe.org/3r9w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r9w RCSB], [http://www.ebi.ac.uk/pdbsum/3r9w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3r9w ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/ERA_AQUAE ERA_AQUAE]] An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism (By similarity). The GTPase is stimulated about 6-fold in the presence of a 12 nucleotide 16S rRNA C-terminal fragment. Mutations in the rRNA sequence obviate stimulation. RNA-binding depends on GTP-binding by the GTPase domain. May function as a checkpoint for assembly of the 30S ribosomal subunit.
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[https://www.uniprot.org/uniprot/ERA_AQUAE ERA_AQUAE] An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism (By similarity). The GTPase is stimulated about 6-fold in the presence of a 12 nucleotide 16S rRNA C-terminal fragment. Mutations in the rRNA sequence obviate stimulation. RNA-binding depends on GTP-binding by the GTPase domain. May function as a checkpoint for assembly of the 30S ribosomal subunit.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Era, composed of a GTPase domain and a K homology domain, is essential for bacterial cell viability. It is required for the maturation of 16S rRNA and assembly of the 30S ribosomal subunit. We showed previously that the protein recognizes nine nucleotides ( ) near the 3' end of 16S rRNA, and that this recognition stimulates GTP-hydrolyzing activity of Era. In all three kingdoms of life, the sequence and helix 45 (h45) (nucleotides 1506-1529) are highly conserved. It has been shown that the to double mutation severely affects the viability of bacteria. However, whether Era interacts with G1530 and/or h45 and whether such interactions (if any) contribute to the stimulation of Era's GTPase activity were not known. Here, we report two RNA structures that contain nucleotides 1506-1542 (RNA301), one in complex with Era and GDPNP (GNP), a nonhydrolysable GTP-analogue, and the other in complex with Era, GNP, and the KsgA methyltransferase. The structures show that Era recognizes 10 nucleotides, including G1530, and that Era also binds h45. Moreover, GTPase assay experiments show that G1530 does not stimulate Era's GTPase activity. Rather, A1531 and A1534 are most important for stimulation and h45 further contributes to the stimulation. Although G1530 does not contribute to the intrinsic GTPase activity of Era, its interaction with Era is important for binding and is essential for the protein to function, leading to the discovery of a new cold-sensitive phenotype of Era.
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The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA.,Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X Proc Natl Acad Sci U S A. 2011 Jun 6. PMID:21646538<ref>PMID:21646538</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3r9w" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aquifex aeolicus huber and stetter 2001]]
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[[Category: Aquifex aeolicus]]
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[[Category: Ji, X]]
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[[Category: Large Structures]]
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[[Category: Tu, C]]
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[[Category: Ji X]]
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[[Category: 16s ribosomal rna]]
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[[Category: Tu C]]
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[[Category: Biogenesis]]
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[[Category: Gtp]]
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[[Category: Gtp hydrolysis]]
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[[Category: Gtpase]]
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[[Category: Hydrolase-rna complex]]
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[[Category: Kh domain]]
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[[Category: Ribosome]]
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Current revision

Crystal structure of Era in complex with MgGDPNP and nucleotides 1506-1542 of 16S ribosomal RNA

PDB ID 3r9w

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