4rle

From Proteopedia

(Difference between revisions)

Revision as of 07:02, 2 March 2023

Crystal structure of the c-di-AMP binding PII-like protein DarA

Structural highlights

4rle is a 1 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. 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

DARA_BACSU Binds cyclic di-AMP (c-di-AMP) and is probably involved in c-di-AMP-mediated signaling pathways. In vitro, can also bind cyclic GMP-AMP (3'3'-cGAMP), with lower affinity, but not c-di-GMP or 2'3'-cGAMP.^[1]

Publication Abstract from PubMed

The cyclic dimeric AMP nucleotide c-di-AMP is an essential second messenger in Bacillus subtilis. We have identified the protein DarA as one of the prominent c-di-AMP receptors in B. subtilis. Crystal structure analysis shows that DarA is highly homologous to PII signal transducer proteins. In contrast to PII proteins the functionally important B and T loops are swapped with respect to their size. DarA is a homo-trimer that binds three molecules of c-di-AMP, each in a pocket located between two subunits. We demonstrate that DarA is capable to bind c-di-AMP and, with lower affinity, also 3'3'-cGAMP, but not c-di-GMP or 2'3'-cGAMP. Consistently the crystal structure shows that within the ligand-binding pocket only one adenine is highly specifically recognized, while the pocket for the other adenine appears to be promiscuous. Comparison with a homologous ligand-free DarA structure reveals that c-di-AMP binding is accompanied by conformational changes of both the fold and the position of the B loop in DarA.

Identification, characterization and structure analysis of the c-di-AMP binding PII-like signal transduction protein DarA.,Gundlach J, Dickmanns A, Schroder-Tittmann K, Neumann P, Kaesler J, Kampf J, Herzberg C, Hammer E, Schwede F, Kaever V, Tittmann K, Stulke J, Ficner R J Biol Chem. 2014 Nov 28. pii: jbc.M114.619619. PMID:25433025^[2]

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

References

↑ Gundlach J, Dickmanns A, Schroder-Tittmann K, Neumann P, Kaesler J, Kampf J, Herzberg C, Hammer E, Schwede F, Kaever V, Tittmann K, Stulke J, Ficner R. Identification, characterization and structure analysis of the c-di-AMP binding PII-like signal transduction protein DarA. J Biol Chem. 2014 Nov 28. pii: jbc.M114.619619. PMID:25433025 doi:http://dx.doi.org/10.1074/jbc.M114.619619
↑ Gundlach J, Dickmanns A, Schroder-Tittmann K, Neumann P, Kaesler J, Kampf J, Herzberg C, Hammer E, Schwede F, Kaever V, Tittmann K, Stulke J, Ficner R. Identification, characterization and structure analysis of the c-di-AMP binding PII-like signal transduction protein DarA. J Biol Chem. 2014 Nov 28. pii: jbc.M114.619619. PMID:25433025 doi:http://dx.doi.org/10.1074/jbc.M114.619619

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/4rle"

Categories: Bacillus subtilis subsp. subtilis str. 168 | Large Structures | Dickmanns A | Ficner R | Neumann P

@@ Line 3: / Line 3: @@
 <StructureSection load='4rle' size='340' side='right'caption='[[4rle]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rle]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RLE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RLE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rle]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RLE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RLE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU00290, yaaQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=4rle FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rle OCA], [https://pdbe.org/4rle PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rle RCSB], [https://www.ebi.ac.uk/pdbsum/4rle PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rle ProSAT]</span></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=4rle FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rle OCA], [http://pdbe.org/4rle PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rle RCSB], [http://www.ebi.ac.uk/pdbsum/4rle PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rle ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DARA_BACSU DARA_BACSU] Binds cyclic di-AMP (c-di-AMP) and is probably involved in c-di-AMP-mediated signaling pathways. In vitro, can also bind cyclic GMP-AMP (3'3'-cGAMP), with lower affinity, but not c-di-GMP or 2'3'-cGAMP.<ref>PMID:25433025</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bacsu]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
 [[Category: Large Structures]]
-[[Category: Dickmanns, A]]
+[[Category: Dickmanns A]]
-[[Category: Ficner, R]]
+[[Category: Ficner R]]
-[[Category: Neumann, P]]
+[[Category: Neumann P]]
-[[Category: Cdiamp]]
-[[Category: Pii-like]]
-[[Category: Unknown function]]

4rle

From Proteopedia

Revision as of 07:02, 2 March 2023

Crystal structure of the c-di-AMP binding PII-like protein DarA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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