4xj3

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Vibrio cholerae DncV GTP bound form

Structural highlights

4xj3 is a 1 chain structure with sequence from Vibrio cholerae O1 biovar El Tor str. N16961. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.65Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DNCV_VIBCH Catalyzes the synthesis of cyclic AMP-GMP from ATP and GTP. Is also able to produce c-di-AMP and c-di-GMP from ATP and GTP, respectively; however, c-AMP-GMP is the dominant molecule produced by DncV in vivo. Is required for efficient V.cholerae intestinal colonization, and down-regulates the colonization-influencing process of chemotaxis. Is not active with dATP, TTP, UTP, and CTP.

Publication Abstract from PubMed

Cyclic dinucleotides (CDNs) play key roles as second messengers and signaling molecules in bacteria and metazoans. The newly identified dinucleotide cyclase in Vibrio cholerae (DncV) produces three different CDNs containing two 3'-5' phosphodiester bonds, and its predominant product is cyclic GMP-AMP, whereas mammalian cyclic GMP-AMP synthase (cGAS) produces only cyclic GMP-AMP containing mixed 2'-5' phosphodiester bonds. We report the crystal structures of V. cholerae and Escherichia coli DncV in complex with various nucleotides in the pre-reaction states. The high-resolution structures revealed that DncV preferably recognizes ATP and GTP as acceptor and donor nucleotides, respectively, in the first nucleotidyl transfer reaction. Considering the recently reported intermediate structures, our pre-reaction state structures provide the precise mechanism of 3'-5' linked cyclic AMP-GMP production in bacteria. A comparison with cGAS in the pre-reaction states suggests that the orientation of the acceptor nucleotide primarily determines the distinct linkage specificities between DncV and cGAS.

Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase.,Kato K, Ishii R, Hirano S, Ishitani R, Nureki O Structure. 2015 Apr 1. pii: S0969-2126(15)00078-7. doi:, 10.1016/j.str.2015.01.023. PMID:25865248^[1]

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

References

↑ Kato K, Ishii R, Hirano S, Ishitani R, Nureki O. Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase. Structure. 2015 Apr 1. pii: S0969-2126(15)00078-7. doi:, 10.1016/j.str.2015.01.023. PMID:25865248 doi:http://dx.doi.org/10.1016/j.str.2015.01.023

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4xj3"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Vibrio cholerae DncV GTP bound form==
-<StructureSection load='4xj3' size='340' side='right' caption='[[4xj3]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+<StructureSection load='4xj3' size='340' side='right'caption='[[4xj3]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xj3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XJ3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xj3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O1_biovar_El_Tor_str._N16961 Vibrio cholerae O1 biovar El Tor str. N16961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XJ3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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]] 1.65&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xj1|4xj1]], [[4xj4|4xj4]], [[4xj5|4xj5]], [[4xj6|4xj6]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=4xj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xj3 OCA], [http://pdbe.org/4xj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xj3 RCSB], [http://www.ebi.ac.uk/pdbsum/4xj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xj3 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=4xj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xj3 OCA], [https://pdbe.org/4xj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xj3 RCSB], [https://www.ebi.ac.uk/pdbsum/4xj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xj3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DNCV_VIBCH DNCV_VIBCH]] Catalyzes the synthesis of cyclic AMP-GMP from ATP and GTP. Is also able to produce c-di-AMP and c-di-GMP from ATP and GTP, respectively; however, c-AMP-GMP is the dominant molecule produced by DncV in vivo. Is required for efficient V.cholerae intestinal colonization, and down-regulates the colonization-influencing process of chemotaxis. Is not active with dATP, TTP, UTP, and CTP.
+[https://www.uniprot.org/uniprot/DNCV_VIBCH DNCV_VIBCH] Catalyzes the synthesis of cyclic AMP-GMP from ATP and GTP. Is also able to produce c-di-AMP and c-di-GMP from ATP and GTP, respectively; however, c-AMP-GMP is the dominant molecule produced by DncV in vivo. Is required for efficient V.cholerae intestinal colonization, and down-regulates the colonization-influencing process of chemotaxis. Is not active with dATP, TTP, UTP, and CTP.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 4xj3" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cyclic GMP-AMP synthase 3D synthase|Cyclic GMP-AMP synthase 3D synthase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ishii, R]]
+[[Category: Large Structures]]
-[[Category: Ishitani, R]]
+[[Category: Vibrio cholerae O1 biovar El Tor str. N16961]]
-[[Category: Kato, K]]
+[[Category: Ishii R]]
-[[Category: Nureki, O]]
+[[Category: Ishitani R]]
-[[Category: Bacterial virulence]]
+[[Category: Kato K]]
-[[Category: Cyclic gmp-amp synthase]]
+[[Category: Nureki O]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Transferase]]

4xj3

From Proteopedia

Current revision

Crystal structure of Vibrio cholerae DncV GTP bound form

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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