[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 basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 2797, Year 2024
Publish dateMar 30, 2024
AuthorsJun-Tao Zhang / Xiao-Yu Liu / Zhuolin Li / Xin-Yang Wei / Xin-Yi Song / Ning Cui / Jirui Zhong / Hongchun Li / Ning Jia /
PubMed AbstractSilent information regulator 2 (Sir2) proteins typically catalyze NAD-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 ...Silent information regulator 2 (Sir2) proteins typically catalyze NAD-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 (DSR2), recognizes the phage tail tube and depletes NAD to abort phage propagation, which is counteracted by the phage-encoded DSR anti-defense 1 (DSAD1), but their molecular mechanisms remain unclear. Here, we determine cryo-EM structures of inactive DSR2 in its apo form, DSR2-DSAD1 and DSR2-DSAD1-NAD, as well as active DSR2-tube and DSR2-tube-NAD complexes. DSR2 forms a tetramer with its C-terminal sensor domains (CTDs) in two distinct conformations: CTD or CTD. Monomeric, rather than oligomeric, tail tube proteins preferentially bind to CTD and activate Sir2 for NAD hydrolysis. DSAD1 binding to CTD allosterically inhibits tube binding and tube-mediated DSR2 activation. Our findings provide mechanistic insight into DSR2 assembly, tube-mediated DSR2 activation, and DSAD1-mediated inhibition and NAD substrate catalysis in bacterial DSR2 anti-phage defense systems.
External linksNat Commun / PubMed:38555355 / PubMed Central
MethodsEM (single particle)
Resolution2.49 - 3.62 Å
Structure data

37919

8wy8

EMDB-37919, PDB-8wy8:
Cryo-EM structure of DSR2 apo complex
Method: EM (single particle) / Resolution: 3.1 Å

37920

8wy9

EMDB-37920, PDB-8wy9:
Cryo-EM structure of DSR2 apo (partial) complex
Method: EM (single particle) / Resolution: 2.57 Å

37921

8wya

EMDB-37921, PDB-8wya:
Cryo-EM structure of DSR2-tube complex
Method: EM (single particle) / Resolution: 3.62 Å

37922

8wyb

EMDB-37922, PDB-8wyb:
Cryo-EM structure of DSR2 (H171A)-tube-NAD+ complex
Method: EM (single particle) / Resolution: 3.37 Å

37923

8wyc

EMDB-37923, PDB-8wyc:
Cryo-EM structure of DSR2 (H171A)-tube-NAD+ (partial) complex
Method: EM (single particle) / Resolution: 3.0 Å

37924

8wyd

EMDB-37924, PDB-8wyd:
Cryo-EM structure of DSR2-DSAD1 complex
Method: EM (single particle) / Resolution: 2.56 Å

37925

8wye

EMDB-37925, PDB-8wye:
Cryo-EM structure of DSR2-DSAD1 (partial) complex
Method: EM (single particle) / Resolution: 2.49 Å

37926

8wyf

EMDB-37926, PDB-8wyf:
Cryo-EM structure of DSR2-DSAD1-NAD+ (partial) complex
Method: EM (single particle) / Resolution: 2.85 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

Source
  • bacillus subtilis (bacteria)
  • bacillus phage spbc2 (virus)
  • bacillus phage spr (virus)
KeywordsANTIVIRAL PROTEIN / Phage defense proteins

+
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