[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

TitleOligomerization of protein arginine methyltransferase 1 and its functional impact on substrate arginine methylation.
Journal, issue, pagesJ Biol Chem, Vol. 300, Issue 12, Page 107947, Year 2024
Publish dateNov 2, 2024
AuthorsTran Dang / Nadendla EswarKumar / Sunil Kumar Tripathi / Chunli Yan / Chun-Hsiung Wang / Mengtong Cao / Tanmoy Kumar Paul / Elizabeth Oladoyin Agboluaje / May P Xiong / Ivaylo Ivanov / Meng-Chiao Ho / Y George Zheng /
PubMed AbstractProtein arginine methyltransferases (PRMTs) are important posttranslational modifying enzymes in eukaryotic proteins and regulate diverse pathways from gene transcription, RNA splicing, and signal ...Protein arginine methyltransferases (PRMTs) are important posttranslational modifying enzymes in eukaryotic proteins and regulate diverse pathways from gene transcription, RNA splicing, and signal transduction to metabolism. Increasing evidence supports that PRMTs exhibit the capacity to form higher-order oligomeric structures, but the structural basis of PRMT oligomerization and its functional consequence are elusive. Herein, we revealed for the first time different oligomeric structural forms of the predominant arginine methyltransferase PRMT1 using cryo-EM, which included tetramer (dimer of dimers), hexamer (trimer of dimers), octamer (tetramer of dimers), decamer (pentamer of dimers), and also helical filaments. Through a host of biochemical assays, we showed that PRMT1 methyltransferase activity was substantially enhanced as a result of the high-ordered oligomerization. High-ordered oligomerization increased the catalytic turnover and the multimethylation processivity of PRMT1. Presence of a catalytically dead PRMT1 mutant also enhanced the activity of WT PRMT1, pointing out a noncatalytic role of oligomerization. Structural modeling demonstrates that oligomerization enhances substrate retention at the PRMT1 surface through electrostatic force. Our studies offered key insights into PRMT1 oligomerization and established that oligomerization constitutes a novel molecular mechanism that positively regulates the enzymatic activity of PRMTs in biology.
External linksJ Biol Chem / PubMed:39491649 / PubMed Central
MethodsEM (single particle) / EM (helical sym.)
Resolution2.55 - 3.56 Å
Structure data

39745

8z2z

EMDB-39745, PDB-8z2z:
PRMT1-Tetramer
Method: EM (single particle) / Resolution: 3.25 Å

39814

8z7h

EMDB-39814, PDB-8z7h:
PRMT1-Decamer
Method: EM (helical sym.) / Resolution: 3.56 Å

39821

8z7o

EMDB-39821, PDB-8z7o:
PRMT1-Filament
Method: EM (single particle) / Resolution: 3.35 Å

44532

9bh4

EMDB-44532, PDB-9bh4:
PRMT1 hexamer, Protein Arginine Methyl transferase
Method: EM (single particle) / Resolution: 2.55 Å

44541

9bhd

EMDB-44541, PDB-9bhd:
PRMT1-Octamer
Method: EM (single particle) / Resolution: 3.38 Å

44546

9bhg

EMDB-44546, PDB-9bhg:
PRMT1-Tetramer
Method: EM (single particle) / Resolution: 3.25 Å

Chemicals

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

Source
  • homo sapiens (human)
  • Escherichia coli BL21(DE3) (bacteria)
KeywordsTRANSFERASE / tetramer / PRMT1-Decamer / PRMT1-Filament / PRMT1 oligomer / PRMT1 Octamer / PRMT1-Tetramer

+
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