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5o5s

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X-ray crystal structure of the RapZ C-terminal domain from Escherichia coli

Structural highlights

5o5s is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.17Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3]

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^[4]

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

References

↑ Kalamorz F, Reichenbach B, Marz W, Rak B, Gorke B. Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli. Mol Microbiol. 2007 Sep;65(6):1518-33. PMID:17824929 doi:http://dx.doi.org/10.1111/j.1365-2958.2007.05888.x
↑ Luciano J, Foulquier E, Fantino JR, Galinier A, Pompeo F. Characterization of YvcJ, a conserved P-loop-containing protein, and its implication in competence in Bacillus subtilis. J Bacteriol. 2009 Mar;191(5):1556-64. doi: 10.1128/JB.01493-08. Epub 2008 Dec 12. PMID:19074378 doi:http://dx.doi.org/10.1128/JB.01493-08
↑ Gopel Y, Papenfort K, Reichenbach B, Vogel J, Gorke B. Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA. Genes Dev. 2013 Mar 1;27(5):552-64. doi: 10.1101/gad.210112.112. PMID:23475961 doi:http://dx.doi.org/10.1101/gad.210112.112
↑ Gonzalez GM, Durica-Mitic S, Hardwick SW, Moncrieffe MC, Resch M, Neumann P, Ficner R, Gorke B, Luisi BF. Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism. Nucleic Acids Res. 2017 Sep 5. doi: 10.1093/nar/gkx732. PMID:28977623 doi:http://dx.doi.org/10.1093/nar/gkx732

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5o5s"

@@ Line 1: / Line 1: @@
 ==X-ray crystal structure of the RapZ C-terminal domain from Escherichia coli==
-<StructureSection load='5o5s' size='340' side='right' caption='[[5o5s]], [[Resolution|resolution]] 1.17&Aring;' scene=''>
+<StructureSection load='5o5s' size='340' side='right'caption='[[5o5s]], [[Resolution|resolution]] 1.17&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5o5s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5o5s]] is a 1 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=5O5S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O5S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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]] 1.17&#8491;</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=5o5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5s OCA], [http://pdbe.org/5o5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5s RCSB], [http://www.ebi.ac.uk/pdbsum/5o5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5s ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=5o5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5s OCA], [https://pdbe.org/5o5s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o5s RCSB], [https://www.ebi.ac.uk/pdbsum/5o5s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5s ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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 ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Durica-Mitic, S]]
+[[Category: Escherichia coli]]
-[[Category: Ficner, R]]
+[[Category: Large Structures]]
-[[Category: Gonzalez, G M]]
+[[Category: Durica-Mitic S]]
-[[Category: Gorke, B]]
+[[Category: Ficner R]]
-[[Category: Hardwick, S W]]
+[[Category: Gonzalez GM]]
-[[Category: Luisi, B F]]
+[[Category: Gorke B]]
-[[Category: Moncrieffe, M]]
+[[Category: Hardwick SW]]
-[[Category: Neumann, P]]
+[[Category: Luisi BF]]
-[[Category: Resch, M]]
+[[Category: Moncrieffe M]]
-[[Category: Chaperone]]
+[[Category: Neumann P]]
-[[Category: Rna binding amino-sugar metabolism kinase like domain pfk like domain]]
+[[Category: Resch M]]

5o5s

From Proteopedia

Current revision

X-ray crystal structure of the RapZ C-terminal domain from Escherichia coli

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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