dnd.md

title: Dnd
layout: article
tableColumns:
    article:
      doi: 10.1038/nchembio.2007.39
      abstract: |
        Modifications of the canonical structures of DNA and RNA play critical roles in cell physiology, DNA replication, transcription and translation in all organisms. We now report that bacterial dnd gene clusters incorporate sulfur into the DNA backbone as a sequence-selective, stereospecific phosphorothioate modification. To our knowledge, unlike any other DNA or RNA modification systems, DNA phosphorothioation by dnd gene clusters is the first physiological modification described on the DNA backbone.
    Sensor: Detecting invading nucleic acid
    Activator: Unknown
    Effector: Nucleic acid degrading
    PFAM: PF00266, PF01507, PF01935, PF08870, PF13476, PF14072

Dnd

Example of genomic structure

The Dnd system have been describe in a total of 2 subsystems.

Here is some example found in the RefSeq database:

Dnd_ABCDE subsystem in the genome of Vibrio tritonius (GCF_001547935.1) is composed of 6 proteins: DndA (WP_068714508.1), DndB (WP_068714510.1), DndC (WP_068714512.1), DndD (WP_068714514.1), DndE (WP_068714516.1)and, DndD (WP_068714526.1).

Dnd_ABCDEFGH subsystem in the genome of Vibrio sp. (GCF_023716625.1) is composed of 8 proteins: DptF (WP_252041715.1), DptG (WP_252041716.1), DptH (WP_252041717.1), DndE (WP_252041720.1), DndD (WP_252041722.1), DndC (WP_252041723.1), DndB (WP_252041724.1)and, DndA (WP_252041725.1).

Distribution of the system among prokaryotes

The Dnd system is present in a total of 218 different species.

Among the 22k complete genomes of RefSeq, this system is present in 388 genomes (1.7 %).

Proportion of genome encoding the Dnd system for the 14 phyla with more than 50 genomes in the RefSeq database. Pie chart of the repartition of all the subsystems found in the RefSeq database.

Structure

Dnd_ABCDE

::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDE,Dnd__DndA,0,DF-plddts_93.47347.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDE,Dnd__DndB,0,DF-plddts_92.88424.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDE,Dnd__DndC,0,DF-plddts_88.29934.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDE,Dnd__DndD,0,DF-plddts_86.40104.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDE,Dnd__DndE,0,DF-plddts_94.0153.pdb

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Dnd_ABCDEFGH

::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptF,0,DF-plddts_90.5398.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptG,0,DF-plddts_92.29053.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptH,0,DF-plddts_83.00895.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndA,0,DF-plddts_95.7234.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndB,0,DF-plddts_94.63597.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndC,0,DF-plddts_90.06321.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndD,0,DF-plddts_85.70431.pdb

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::molstar-pdbe-plugin

height: 700 dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndE,0,DF-plddts_95.24932.pdb

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Experimental validation

graph LR; Xiong_2019[Xiong et al., 2019] --> Origin_0 Origin_0[ DndCDEA-PbeABCD Halalkalicoccus jeotgali] --> Expressed_0[Natrinema sp. CJ7-F] Expressed_0[Natrinema sp. CJ7-F] ----> SNJ1 subgraph Title1[Reference] Xiong_2019 end subgraph Title2[System origin] Origin_0 end subgraph Title3[Expression species] Expressed_0 end subgraph Title4[Phage infected] SNJ1 end style Title1 fill:none,stroke:none,stroke-width:none style Title2 fill:none,stroke:none,stroke-width:none style Title3 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none ## Relevant abstracts

::relevant-abstracts

items: - doi: 10.1038/nchembio.2007.39 - doi: 10.1038/s41467-019-09390-9

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