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5np9

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Crystal structure of Bacillus subtilis YdiB in complex with ADP

Structural highlights

5np9 is a 1 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TSAE_BACSU Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaB; this reaction does not require ATP in vitro. TsaE seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. Displays ATPase activity in vitro, which is modulated by the oligomeric status of the protein.^[1] ^[2]

Publication Abstract from PubMed

Fine-tuning of signaling pathways is essential for cells to cope with sudden environmental variations. This delicate balance is maintained in particular by protein kinases that control the activity of target proteins by reversible phosphorylation. In addition to homologous eukaryotic enzymes, bacteria have evolved some specific Ser/Thr/Tyr protein kinases without any structural resemblance to their eukaryotic counterparts. Here, we show that a previously identified family of ATPases, broadly conserved among bacteria, is in fact a new family of protein kinases with a Ser/Thr/Tyr kinase activity. A prototypic member of this family, YdiB from Bacillus subtilis, is able to autophosphorylate and to phosphorylate a surrogate substrate, the myelin basic protein. Two crystal structures of YdiB were solved (1.8 and 2.0A) that display a unique ATP-binding fold unrelated to known protein-kinases although a conserved HxD motif is reminiscent of that found in Hanks-type protein kinases. The effect of mutations of conserved residues further highlights the unique nature of this new protein kinase family that we name UbK (Ubiquitous bacterial Kinase). We investigated the cellular role of YdiB and showed that a ydiB mutant was more sensitive to paraquat treatment than the wild-type with ~13% of cells with an aberrant morphology. Additionally, YdiE which is known to participate with both YdiC and YdiB in an essential chemical modification of some specific tRNAs, is phosphorylated in vitro by YdiB. These results expand the boundaries of the bacterial kinome and support the involvement of YdiB in protein translation and resistance to oxidative stress in B. subtilis.

Expanding the kinome world: A new protein kinase family widely conserved in bacteria.,Nguyen HA, El Khoury T, Guiral S, Laaberki MH, Candusso MP, Galisson F, Foucher AE, Kesraoui S, Ballut L, Vallet S, Orelle C, Zucchini L, Martin J, Page A, Attieh J, Aghajari N, Grangeasse C, Jault JM J Mol Biol. 2017 Sep 7. pii: S0022-2836(17)30422-9. doi:, 10.1016/j.jmb.2017.08.016. PMID:28890133^[3]

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

References

↑ Karst JC, Foucher AE, Campbell TL, Di Guilmi AM, Stroebel D, Mangat CS, Brown ED, Jault JM. The ATPase activity of an 'essential' Bacillus subtilis enzyme, YdiB, is required for its cellular function and is modulated by oligomerization. Microbiology. 2009 Mar;155(Pt 3):944-56. PMID:19246765 doi:http://dx.doi.org/155/3/944
↑ Lauhon CT. Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry. 2012 Nov 6;51(44):8950-63. doi: 10.1021/bi301233d. Epub 2012 Oct, 26. PMID:23072323 doi:http://dx.doi.org/10.1021/bi301233d
↑ Nguyen HA, El Khoury T, Guiral S, Laaberki MH, Candusso MP, Galisson F, Foucher AE, Kesraoui S, Ballut L, Vallet S, Orelle C, Zucchini L, Martin J, Page A, Attieh J, Aghajari N, Grangeasse C, Jault JM. Expanding the kinome world: A new protein kinase family widely conserved in bacteria. J Mol Biol. 2017 Sep 7. pii: S0022-2836(17)30422-9. doi:, 10.1016/j.jmb.2017.08.016. PMID:28890133 doi:http://dx.doi.org/10.1016/j.jmb.2017.08.016

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/5np9"

Categories: Bacillus subtilis | Large Structures | Aghajari N | Ballut L

@@ Line 1: / Line 1: @@
 ==Crystal structure of Bacillus subtilis YdiB in complex with ADP==
-<StructureSection load='5np9' size='340' side='right' caption='[[5np9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5np9' size='340' side='right'caption='[[5np9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5np9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NP9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NP9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5np9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NP9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5mvr|5mvr]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5np9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5np9 OCA], [http://pdbe.org/5np9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5np9 RCSB], [http://www.ebi.ac.uk/pdbsum/5np9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5np9 ProSAT]</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=5np9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5np9 OCA], [https://pdbe.org/5np9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5np9 RCSB], [https://www.ebi.ac.uk/pdbsum/5np9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5np9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TSAE_BACSU TSAE_BACSU]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaB; this reaction does not require ATP in vitro. TsaE seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. Displays ATPase activity in vitro, which is modulated by the oligomeric status of the protein.<ref>PMID:19246765</ref> <ref>PMID:23072323</ref>
+[https://www.uniprot.org/uniprot/TSAE_BACSU TSAE_BACSU] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaB; this reaction does not require ATP in vitro. TsaE seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. Displays ATPase activity in vitro, which is modulated by the oligomeric status of the protein.<ref>PMID:19246765</ref> <ref>PMID:23072323</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Aghajari, N]]
+[[Category: Bacillus subtilis]]
-[[Category: Ballut, L]]
+[[Category: Large Structures]]
-[[Category: Adp]]
+[[Category: Aghajari N]]
-[[Category: Kinase]]
+[[Category: Ballut L]]
-[[Category: Phosphorylastion]]
-[[Category: Transferase]]

5np9

From Proteopedia

Current revision

Crystal structure of Bacillus subtilis YdiB in complex with ADP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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