5o5q
From Proteopedia
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==X-ray crystal structure of RapZ from Escherichia coli (P3221 space group)== | ==X-ray crystal structure of RapZ from Escherichia coli (P3221 space group)== | ||
| - | <StructureSection load='5o5q' size='340' side='right' caption='[[5o5q]], [[Resolution|resolution]] 3.25Å' scene=''> | + | <StructureSection load='5o5q' size='340' side='right'caption='[[5o5q]], [[Resolution|resolution]] 3.25Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5o5q]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5Q OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[5o5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O5Q FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 3.25Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5o5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5q OCA], [https://pdbe.org/5o5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o5q RCSB], [https://www.ebi.ac.uk/pdbsum/5o5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5q ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/RAPZ_ECOLI RAPZ_ECOLI] Modulates the synthesis of GlmS, by affecting the processing and stability of the regulatory small RNA GlmZ. When glucosamine-6-phosphate (GlcN6P) concentrations are high in the cell, RapZ binds GlmZ and targets it to cleavage by RNase E. Consequently, GlmZ is inactivated and unable to activate GlmS synthesis. Under low GlcN6P concentrations, RapZ is sequestered and inactivated by an other regulatory small RNA, GlmY, preventing GlmZ degradation and leading to synthesis of GlmS (PubMed:17824929, PubMed:23475961). Displays ATPase and GTPase activities in vitro. Can also hydrolyze pNPP (PubMed:19074378).<ref>PMID:17824929</ref> <ref>PMID:19074378</ref> <ref>PMID:23475961</ref> |
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | In phylogenetically diverse bacteria, the conserved protein RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism. RapZ contributes to the control of glucosamine phosphate biogenesis by selectively presenting the regulatory small RNA GlmZ to the essential ribonuclease RNase E for inactivation. Here, we report the crystal structures of full length Escherichia coli RapZ at 3.40 A and 3.25 A, and its isolated C-terminal domain at 1.17 A resolution. The structural data confirm that the N-terminal domain of RapZ possesses a kinase fold, whereas the C-terminal domain bears closest homology to a subdomain of 6-phosphofructokinase, an important enzyme in the glycolytic pathway. RapZ self-associates into a domain swapped dimer of dimers, and in vivo data support the importance of quaternary structure in RNA-mediated regulation of target gene expression. Based on biochemical, structural and genetic data, we suggest a mechanism for binding and presentation by RapZ of GlmZ and the closely related decoy sRNA, GlmY. We discuss a scenario for the molecular evolution of RapZ through re-purpose of enzyme components from central metabolism. | ||
| + | |||
| + | Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.,Gonzalez GM, Durica-Mitic S, Hardwick SW, Moncrieffe MC, Resch M, Neumann P, Ficner R, Gorke B, Luisi BF Nucleic Acids Res. 2017 Sep 5. doi: 10.1093/nar/gkx732. PMID:28977623<ref>PMID:28977623</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5o5q" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Durica-Mitic | + | [[Category: Escherichia coli]] |
| - | [[Category: Ficner | + | [[Category: Large Structures]] |
| - | [[Category: Gonzalez | + | [[Category: Durica-Mitic S]] |
| - | [[Category: Gorke | + | [[Category: Ficner R]] |
| - | [[Category: Hardwick | + | [[Category: Gonzalez GM]] |
| - | [[Category: Luisi | + | [[Category: Gorke B]] |
| - | [[Category: Moncrieffe | + | [[Category: Hardwick SW]] |
| - | [[Category: Neumann | + | [[Category: Luisi BF]] |
| - | [[Category: Resch | + | [[Category: Moncrieffe M]] |
| - | + | [[Category: Neumann P]] | |
| - | + | [[Category: Resch M]] | |
Current revision
X-ray crystal structure of RapZ from Escherichia coli (P3221 space group)
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