7odx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:49, 1 February 2024) (edit) (undo)
 
Line 1: Line 1:
-
'''Unreleased structure'''
 
-
The entry 7odx is ON HOLD until Paper Publication
+
==Cyanophage S-2L Succinoaminodeoxyadenylate synthetase (PurZ) bound to dGMP and dATP as an energy donor==
 +
<StructureSection load='7odx' size='340' side='right'caption='[[7odx]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[7odx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cyanophage_S-2L Cyanophage S-2L]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ODX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ODX FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6961708&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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=7odx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7odx OCA], [https://pdbe.org/7odx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7odx RCSB], [https://www.ebi.ac.uk/pdbsum/7odx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7odx ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PURZ_BPS2L PURZ_BPS2L] Involved in the synthesis of the atypical nucleotide dZTP (2-amino-2'-deoxyadenosine-5'-triphosphate) (PubMed:33926955). Catalyzes the condensation of aspartate with deoxyguanylate into dSMP (N6-succino-2-amino-2'-deoxyadenylate), which undergoes defumarylation and phosphorylation respectively by host PurB and guanylate/nucleoside diphosphate kinases to give dZTP (PubMed:33926955). dZTP is integrated into the viral genome instead of adenine by the viral DNA polymerase. This Z-base probably completely replaces adenosine and forms a triple bond to the opposite T-base (PubMed:33926955). The resulting non-standard viral DNA is called Z-genome (PubMed:33926955). The chemically modified DNA is probably harder for the host bacteria to digest with nucleases or restriction enzymes (Probable).[HAMAP-Rule:MF_04166]<ref>PMID:33926955</ref>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Cyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes - datZ, mazZ and purZ - was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.
-
Authors:
+
Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA.,Czernecki D, Bonhomme F, Kaminski PA, Delarue M Nat Commun. 2021 Aug 5;12(1):4710. doi: 10.1038/s41467-021-25064-x. PMID:34354070<ref>PMID:34354070</ref>
-
Description:
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
[[Category: Unreleased Structures]]
+
</div>
 +
<div class="pdbe-citations 7odx" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Cyanophage S-2L]]
 +
[[Category: Large Structures]]
 +
[[Category: Czernecki D]]
 +
[[Category: Delarue M]]

Current revision

Cyanophage S-2L Succinoaminodeoxyadenylate synthetase (PurZ) bound to dGMP and dATP as an energy donor

PDB ID 7odx

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools