[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural insights into activation mechanisms on NADase of the bacterial DSR2 anti-phage defense system.
Journal, issue, pagesSci Adv, Vol. 10, Issue 31, Page eadn5691, Year 2024
Publish dateAug 2, 2024
AuthorsHong Zhang / Yu Li / Lanlan Li / Lifei Chen / Chunhua Zhu / Lifang Sun / Panpan Dong / Dingding Jing / Jinbo Yang / Lei Fu / Fangnan Xiao / Ningshao Xia / Shaowei Li / Qingbing Zheng / Yunkun Wu /
PubMed AbstractAs a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD) of ...As a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD) of infected cells, which can be activated by tail tube protein (TTP) and inhibited by DSR anti-defense 1 (DSAD1) of diverse phages. However, the regulating mechanism remains elusive. Here, we determined the cryo-electron microscopy structure of apo DSR2, as well as the respective complex structures with TTP and DSAD1. Structural analyses and biochemical studies reveal that DSR2 forms a tetramer with a SIR2 central core and two distinct conformations. Monomeric TTP preferentially binds to the closed conformation of DSR2, inducing conformational distortions on SIR2 tetramer assembly to activate its NADase activity. DSAD1 combines with the open conformation of DSR2, directly or allosterically inhibiting TTP activation on DSR2 NAD hydrolysis. Our findings decipher the detailed molecule mechanisms for DSR2 NADase activity regulation and lay a foundation for in-depth understanding of the DSR2 anti-phage defense system.
External linksSci Adv / PubMed:39083599 / PubMed Central
MethodsEM (single particle)
Resolution2.92 - 6.99 Å
Structure data

38297

8xew

EMDB-38297, PDB-8xew:
Cryo-EM structure of defence-associatedsirtuin 2 (DSR2) H171A protein
Method: EM (single particle) / Resolution: 2.92 Å

38302

8xfe

EMDB-38302, PDB-8xfe:
Cryo-EM structure of defence-associated sirtuin 2 (DSR2) H171A protein in complex with DSR anti-defence 1(DSAD1)
Method: EM (single particle) / Resolution: 2.98 Å

38303

8xff

EMDB-38303, PDB-8xff:
Cryo-EM structure of defence-associatedsirtuin 2 (DSR2) H171A protein in complex with SPR phage tail tube protein
Method: EM (single particle) / Resolution: 3.16 Å

EMDB-38397: Intact MAP of defence-associated sirtuin 2 (DSR2) H171A protein in complex with DSAD1 (DSR anti-defence 1)
Method: EM (single particle) / Resolution: 6.99 Å

Source
  • bacillus sp. dsm 5850 (bacteria)
  • phage #d (virus)
KeywordsCELL INVASION / Cryo-EM / defence-associated sirtuin 2 (DSR2) protein / Sir2 / defence-associated sirtuin (DSR)DSR2 / DSR anti-defence 1(DSAD1) / Phage invasion / SPR phage tail tube

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more