5m04
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Structure of ObgE from Escherichia coli== | |
| + | <StructureSection load='5m04' size='340' side='right'caption='[[5m04]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5m04]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH5alpha Escherichia coli DH5alpha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M04 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m04 OCA], [https://pdbe.org/5m04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m04 RCSB], [https://www.ebi.ac.uk/pdbsum/5m04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m04 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/OBG_ECOLI OBG_ECOLI] An abundant, essential GTPase which binds GTP, GDP and ppGpp with moderate affinity, shows high guanine nucleotide exchange rate constants for GTP and GDP, and has a relatively low GTP hydrolysis rate. It is estimated there are 34000 molecules in log-phase cells and 5600 molecules in stationary-phase cells as the monomer. Required for chromosome segregation. It also plays a role in the stringent response, and a non-essential role in the late steps of ribosome biogenesis, but how it performs these functions remains unelucidated.<ref>PMID:11555285</ref> <ref>PMID:12402086</ref> <ref>PMID:11976298</ref> <ref>PMID:12855728</ref> <ref>PMID:12826057</ref> <ref>PMID:15836769</ref> <ref>PMID:15721258</ref> <ref>PMID:16518617</ref> <ref>PMID:16980477</ref> <ref>PMID:17616600</ref> <ref>PMID:17578452</ref> <ref>PMID:19555460</ref> Required for correct chromosome partitioning; in temperature-sensitive (ts) mutant nucleoids do not partition but remain in the middle of cell, cells elongate but do not divide. Overexpression protects cells against UV damage. Ts mutants have impaired plasmid and lamdba phage replication, possibly via effects on DnaA. Regulates DnaA levels. Genetic interactions of Val-168 and a C-terminal insertion mutant with the double-strand break repair factors recA and recBCD, and with seqA suggests that ObgE, either directly or indirectly, promotes replication fork stability. Initiation of DNA replication continues in ObgE-depleted cells.<ref>PMID:11555285</ref> <ref>PMID:12402086</ref> <ref>PMID:11976298</ref> <ref>PMID:12855728</ref> <ref>PMID:12826057</ref> <ref>PMID:15836769</ref> <ref>PMID:15721258</ref> <ref>PMID:16518617</ref> <ref>PMID:16980477</ref> <ref>PMID:17616600</ref> <ref>PMID:17578452</ref> <ref>PMID:19555460</ref> Binds to pre-50S ribosomal subunits in a salt-dependent manner, has also been seen associated with 30S subunits. Overexpression rescues an rrmJ deletion stabilizing the 70S ribosome. Even at permissive temperatures the ts mutant (Gln-80/Asn-85) shows disrupted 50S ribosomal subunit assembly, defects in 16 and 23S rRNA processing and altered association of some late-assembling ribosomal proteins. Dissociates from the pre-50S ribosome under conditions of amino acid starvation. The levels of (p)ppGpp rise in the ts mutant (Gln-80/Asn-85), possibly because ObgE controls SpoT. Binds GDP and ppGpp with the same affinity. During ribosome assembly ObgE acts later than the rRNA methyltransferase rrmj and DEAD-box RNA helicases DeaD and SrmB.<ref>PMID:11555285</ref> <ref>PMID:12402086</ref> <ref>PMID:11976298</ref> <ref>PMID:12855728</ref> <ref>PMID:12826057</ref> <ref>PMID:15836769</ref> <ref>PMID:15721258</ref> <ref>PMID:16518617</ref> <ref>PMID:16980477</ref> <ref>PMID:17616600</ref> <ref>PMID:17578452</ref> <ref>PMID:19555460</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The Obg protein family belongs to the TRAFAC (translation factor) class of P-loop GTPases and is conserved from bacteria to eukaryotes. Essential roles in many different cellular processes have been suggested for the Obg protein from Escherichia coli (ObgE), and we recently showed that it is a central regulator of bacterial persistence. Here, we report the first crystal structure of ObgE at 1.85 A resolution in the GDP-bound state, showing the characteristic N-terminal domain and a central G domain that are common to all Obg proteins. ObgE also contains an intrinsically disordered C-terminal domain, and we show here that this domain specifically contributed to GTP binding, while it did not influence GDP binding or GTP hydrolysis. Biophysical analysis, using small angle X-ray scattering and multi-angle light scattering experiments, revealed that ObgE is a monomer in solution, regardless of the bound nucleotide. In contrast to recent suggestions, our biochemical analyses further indicate that ObgE is neither activated by K+ ions nor by homodimerization. However, the ObgE GTPase activity was stimulated upon binding to the ribosome, confirming the ribosome-dependent GTPase activity of the Obg family. Combined, our data represent an important step toward further unraveling the detailed molecular mechanism of ObgE, which might pave the way to further studies into how this GTPase regulates bacterial physiology, including persistence. | ||
| - | + | Structural and Biochemical Analysis of Escherichia coli ObgE, a Central Regulator of Bacterial Persistence.,Gkekas S, Singh RK, Shkumatov AV, Messens J, Fauvart M, Verstraeten N, Michiels J, Versees W J Biol Chem. 2017 Feb 21. pii: jbc.M116.761809. doi: 10.1074/jbc.M116.761809. PMID:28223358<ref>PMID:28223358</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 5m04" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Gkekas S]] | ||
| + | [[Category: Singh RK]] | ||
| + | [[Category: Versees W]] | ||
Current revision
Structure of ObgE from Escherichia coli
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