6fko

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Current revision (12:29, 9 May 2024) (edit) (undo)
 
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<StructureSection load='6fko' size='340' side='right'caption='[[6fko]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='6fko' size='340' side='right'caption='[[6fko]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6fko]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6fjr 6fjr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FKO FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6fko]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_phage_phiVC8 Vibrio phage phiVC8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6fjr 6fjr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FKO FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=HDA:HADACIDIN'>HDA</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]] 2.1&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6fjr|6fjr]]</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=HDA:HADACIDIN'>HDA</scene></td></tr>
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<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=6fko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fko OCA], [http://pdbe.org/6fko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fko RCSB], [http://www.ebi.ac.uk/pdbsum/6fko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fko ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6fko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fko OCA], [https://pdbe.org/6fko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fko RCSB], [https://www.ebi.ac.uk/pdbsum/6fko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fko 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>
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==See Also==
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*[[Adenylosuccinate synthetase 3D structures|Adenylosuccinate synthetase 3D structures]]
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== References ==
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<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Haouz, A]]
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[[Category: Vibrio phage phiVC8]]
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[[Category: Kaminski, P A]]
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[[Category: Haouz A]]
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[[Category: Sleiman, D]]
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[[Category: Kaminski PA]]
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[[Category: H, J Loc]]
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[[Category: Loc'h J]]
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[[Category: 6-diaminopurine]]
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[[Category: Sleiman D]]
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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 ATP, dGMP, hadacidin at 2.1 Angstrom resolution

PDB ID 6fko

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