6flf: Difference between revisions
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<StructureSection load='6flf' size='340' side='right'caption='[[6flf]], [[Resolution|resolution]] 1.33Å' scene=''> | <StructureSection load='6flf' size='340' side='right'caption='[[6flf]], [[Resolution|resolution]] 1.33Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6flf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[6flf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_phage_phiVC8 Vibrio phage phiVC8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FLF FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.33Å</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=6flf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6flf OCA], [https://pdbe.org/6flf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6flf RCSB], [https://www.ebi.ac.uk/pdbsum/6flf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6flf 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=6flf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6flf OCA], [https://pdbe.org/6flf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6flf RCSB], [https://www.ebi.ac.uk/pdbsum/6flf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6flf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/PURZ_BPVC8 PURZ_BPVC8] Involved in the synthesis of the atypical nucleotide dZTP (2-amino-2'-deoxyadenosine-5'-triphosphate) (PubMed:33926954). 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:33926954</ref> <ref>PMID:33926955</ref> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Vibrio phage | [[Category: Vibrio phage phiVC8]] | ||
[[Category: Haouz | [[Category: Haouz A]] | ||
[[Category: Kaminski | [[Category: Kaminski PA]] | ||
[[Category: | [[Category: Loc'h J]] | ||
[[Category: Sleiman D]] | |||
[[Category: | |||
Latest revision as of 15:29, 9 May 2024
Deoxyguanylosuccinate synthase (DgsS) structure at 1.33 Angstrom resolution.Deoxyguanylosuccinate synthase (DgsS) structure at 1.33 Angstrom resolution.
Structural highlights
FunctionPURZ_BPVC8 Involved in the synthesis of the atypical nucleotide dZTP (2-amino-2'-deoxyadenosine-5'-triphosphate) (PubMed:33926954). 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][1] [2] Publication Abstract from PubMedCells have two purine pathways that synthesize adenine and guanine ribonucleotides from phosphoribose via inosylate. A chemical hybrid between adenine and guanine, 2-aminoadenine (Z), replaces adenine in the DNA of the cyanobacterial virus S-2L. We show that S-2L and Vibrio phage PhiVC8 encode a third purine pathway catalyzed by PurZ, a distant paralog of succinoadenylate synthase (PurA), the enzyme condensing aspartate and inosylate in the adenine pathway. PurZ condenses aspartate with deoxyguanylate into dSMP (N6-succino-2-amino-2'-deoxyadenylate), which undergoes defumarylation and phosphorylation to give dZTP (2-amino-2'-deoxyadenosine-5'-triphosphate), a substrate for the phage DNA polymerase. Crystallography and phylogenetics analyses indicate a close relationship between phage PurZ and archaeal PurA enzymes. Our work elucidates the biocatalytic innovation that remodeled a DNA building block beyond canonical molecular biology. A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes.,Sleiman D, Garcia PS, Lagune M, Loc'h J, Haouz A, Taib N, Rothlisberger P, Gribaldo S, Marliere P, Kaminski PA Science. 2021 Apr 30;372(6541):516-520. doi: 10.1126/science.abe6494. PMID:33926955[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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