6rm2: Difference between revisions

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'''Unreleased structure'''


The entry 6rm2 is ON HOLD
==Deoxyguanylosuccinate synthase (DgsS) structure with ATP, IMP, Magnesium==
<StructureSection load='6rm2' size='340' side='right'caption='[[6rm2]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6rm2]] 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=6RM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RM2 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]] 2.5&#8491;</td></tr>
<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=IMP:INOSINIC+ACID'>IMP</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=6rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rm2 OCA], [https://pdbe.org/6rm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rm2 RCSB], [https://www.ebi.ac.uk/pdbsum/6rm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rm2 ProSAT]</span></td></tr>
</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>


Authors:  
==See Also==
 
*[[Adenylosuccinate synthetase 3D structures|Adenylosuccinate synthetase 3D structures]]
Description:  
== References ==
[[Category: Unreleased Structures]]
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Vibrio phage phiVC8]]
[[Category: Haouz A]]
[[Category: Kaminski PA]]
[[Category: Loc'h J]]
[[Category: Sleiman D]]

Latest revision as of 15:23, 24 January 2024

Deoxyguanylosuccinate synthase (DgsS) structure with ATP, IMP, MagnesiumDeoxyguanylosuccinate synthase (DgsS) structure with ATP, IMP, Magnesium

Structural highlights

6rm2 is a 2 chain structure with sequence from Vibrio phage phiVC8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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][1] [2]

See Also

References

  1. Zhou Y, Xu X, Wei Y, Cheng Y, Guo Y, Khudyakov I, Liu F, He P, Song Z, Li Z, Gao Y, Ang EL, Zhao H, Zhang Y, Zhao S. A widespread pathway for substitution of adenine by diaminopurine in phage genomes. Science. 2021 Apr 30;372(6541):512-516. doi: 10.1126/science.abe4882. PMID:33926954 doi:http://dx.doi.org/10.1126/science.abe4882
  2. Sleiman D, Garcia PS, Lagune M, Loc'h J, Haouz A, Taib N, Rothlisberger P, Gribaldo S, Marliere P, Kaminski PA. A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes. Science. 2021 Apr 30;372(6541):516-520. doi: 10.1126/science.abe6494. PMID:33926955 doi:http://dx.doi.org/10.1126/science.abe6494

6rm2, resolution 2.50Å

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