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5ded

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Revision as of 10:32, 21 June 2023

Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp

Structural highlights

5ded is a 8 chain structure with sequence from Bacillus subtilis PY79. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YJBM_BACSU Functions as a (p)ppGpp synthase. In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. YjbM has probably a minor role in stringent response.^[1]

Publication Abstract from PubMed

Nucleotide-based second messengers serve in the response of living organisms to environmental changes. In bacteria and plant chloroplasts, guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) [collectively named "(p)ppGpp"] act as alarmones that globally reprogram cellular physiology during various stress conditions. Enzymes of the RelA/SpoT homology (RSH) family synthesize (p)ppGpp by transferring pyrophosphate from ATP to GDP or GTP. Little is known about the catalytic mechanism and regulation of alarmone synthesis. It also is unclear whether ppGpp and pppGpp execute different functions. Here, we unravel the mechanism and allosteric regulation of the highly cooperative alarmone synthetase small alarmone synthetase 1 (SAS1) from Bacillus subtilis. We determine that the catalytic pathway of (p)ppGpp synthesis involves a sequentially ordered substrate binding, activation of ATP in a strained conformation, and transfer of pyrophosphate through a nucleophilic substitution (SN2) reaction. We show that pppGpp-but not ppGpp-positively regulates SAS1 at an allosteric site. Although the physiological significance remains to be elucidated, we establish the structural and mechanistic basis for a biological activity in which ppGpp and pppGpp execute different functional roles.

Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone.,Steinchen W, Schuhmacher JS, Altegoer F, Fage CD, Srinivasan V, Linne U, Marahiel MA, Bange G Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13348-53. doi:, 10.1073/pnas.1505271112. Epub 2015 Oct 12. PMID:26460002^[2]

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

References

↑ Nanamiya H, Kasai K, Nozawa A, Yun CS, Narisawa T, Murakami K, Natori Y, Kawamura F, Tozawa Y. Identification and functional analysis of novel (p)ppGpp synthetase genes in Bacillus subtilis. Mol Microbiol. 2008 Jan;67(2):291-304. Epub 2007 Dec 7. PMID:18067544 doi:http://dx.doi.org/10.1111/j.1365-2958.2007.06018.x
↑ Steinchen W, Schuhmacher JS, Altegoer F, Fage CD, Srinivasan V, Linne U, Marahiel MA, Bange G. Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone. Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13348-53. doi:, 10.1073/pnas.1505271112. Epub 2015 Oct 12. PMID:26460002 doi:http://dx.doi.org/10.1073/pnas.1505271112

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/5ded"

@@ Line 3: / Line 3: @@
 <StructureSection load='5ded' size='340' side='right'caption='[[5ded]], [[Resolution|resolution]] 2.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ded]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DED OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DED FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ded]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_PY79 Bacillus subtilis PY79]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DED FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0O2:GUANOSINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)+3-(TRIHYDROGEN+DIPHOSPHATE)'>0O2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/GTP_diphosphokinase GTP diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.5 2.7.6.5] </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=5ded FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ded OCA], [https://pdbe.org/5ded PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ded RCSB], [https://www.ebi.ac.uk/pdbsum/5ded PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ded ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ded FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ded OCA], [http://pdbe.org/5ded PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ded RCSB], [http://www.ebi.ac.uk/pdbsum/5ded PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ded ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YJBM_BACSU YJBM_BACSU]] Functions as a (p)ppGpp synthase. In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. YjbM has probably a minor role in stringent response.<ref>PMID:18067544</ref>
+[https://www.uniprot.org/uniprot/YJBM_BACSU YJBM_BACSU] Functions as a (p)ppGpp synthase. In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. YjbM has probably a minor role in stringent response.<ref>PMID:18067544</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: GTP diphosphokinase]]
+[[Category: Bacillus subtilis PY79]]
 [[Category: Large Structures]]
-[[Category: Altegoer, F]]
+[[Category: Altegoer F]]
-[[Category: Bange, G]]
+[[Category: Bange G]]
-[[Category: Schuhmacher, J S]]
+[[Category: Schuhmacher JS]]
-[[Category: Steinchen, W]]
+[[Category: Steinchen W]]
-[[Category: Alarmone]]
-[[Category: Allosteric regulator]]
-[[Category: Stringent response]]
-[[Category: Transferase]]

5ded

From Proteopedia

Revision as of 10:32, 21 June 2023

Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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