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6tnh

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Current revision (13:05, 24 January 2024) (edit) (undo)
 
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<StructureSection load='6tnh' size='340' side='right'caption='[[6tnh]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
<StructureSection load='6tnh' size='340' side='right'caption='[[6tnh]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6tnh]] is a 2 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=6TNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TNH FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6tnh]] is a 2 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=6TNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TNH FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.21&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phiVC8_p27 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1076759 Vibrio phage phiVC8])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6tnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tnh OCA], [https://pdbe.org/6tnh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tnh RCSB], [https://www.ebi.ac.uk/pdbsum/6tnh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tnh 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=6tnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tnh OCA], [https://pdbe.org/6tnh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tnh RCSB], [https://www.ebi.ac.uk/pdbsum/6tnh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tnh ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
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[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]]
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[[Category: Vibrio phage phivc8]]
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[[Category: Vibrio phage phiVC8]]
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[[Category: Haouz, A]]
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[[Category: Haouz A]]
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[[Category: Kaminski, P A]]
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[[Category: Kaminski PA]]
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[[Category: Sleiman, D]]
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[[Category: Loc'h J]]
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[[Category: H, J Loc]]
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[[Category: Sleiman D]]
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[[Category: 6-diaminopurine]]
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[[Category: Biosynthetic protein]]
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[[Category: Phage phivc8]]
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[[Category: Synthetase]]
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Current revision

Deoxyguanylosuccinate synthase (DgsS) quaternary structure with AMPPcP, dGMP, Asp, Magnesium at 2.21 Angstrom resolution

PDB ID 6tnh

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