[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

TitleActinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 118, Issue 48, Year 2021
Publish dateNov 30, 2021
AuthorsEduardo M Bruch / Pierre Vilela / Lu Yang / Alexandra Boyko / Norik Lexa-Sapart / Bertrand Raynal / Pedro M Alzari / Marco Bellinzoni /
PubMed Abstractα-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, ...α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, all considered to be structured around a high-molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix bearing an actinobacterial specific insertion that precludes larger protein oligomerization. This particular feature, together with the presence of an gene coding for both the decarboxylase and the acyltransferase domains on the same polypetide, is spread over Actinobacteria and reflects the association of PDH and ODH into a single physical complex. Considering the central role of the pyruvate and 2-oxoglutarate nodes in central metabolism, our findings pave the way to both therapeutic and metabolic engineering applications.
External linksProc Natl Acad Sci U S A / PubMed:34819376 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.35 - 3.92 Å
Structure data

EMDB-11600:
Cubic core of the dihydrolipoamide acyltransferase (E2b) component of the branched-chain alpha-ketoacid dehydrogenase complex (BCKDH) from M. tuberculosis
Method: EM (single particle) / Resolution: 3.92 Å

PDB-6zzi:
Crystal structure of the catalyic domain of Corynebacterium glutamicum acetyltransferase AceF (E2p).
Method: X-RAY DIFFRACTION / Resolution: 1.932 Å

PDB-6zzj:
Crystal structure of the catalytic domain of Corynebacterium glutamicum acetyltransferase AceF (E2p) in complex with oxidized CoA.
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-6zzk:
Crystal structure of the catalytic domain of C. glutamicum AceF (E2p) in ternary complex with CoA and dihydrolipoamide.
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-6zzl:
Crystal structure of the catalytic domain plus N-terminal linker of the acetyltransferase AceF (E2p) from Corynebacterium glutamicum.
Method: X-RAY DIFFRACTION / Resolution: 2.229 Å

PDB-6zzm:
Crystal structure of the catalytic domain of Corynebacterium mustelae predicted acetyltransferase AceF (E2p).
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-6zzn:
Crystal structure of the cubic catalytic core of the Mycobacterium tuberculosis branched-chain alphaketoacid acyltransferase component (E2b).
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-CAO:
OXIDIZED COENZYME A

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

ChemComp-COA:
COENZYME A

ChemComp-LPM:
6,8-DIMERCAPTO-OCTANOIC ACID AMIDE

ChemComp-GOL:
GLYCEROL

ChemComp-PO4:
PHOSPHATE ION

ChemComp-ACT:
ACETATE ION

ChemComp-IMD:
IMIDAZOLE

Source
  • mycobacterium tuberculosis h37rv (bacteria)
  • corynebacterium glutamicum (strain atcc 13032 / dsm 20300 / jcm 1318 / lmg 3730 / ncimb 10025) (bacteria)
  • corynebacterium glutamicum atcc 13032 (bacteria)
  • corynebacterium mustelae (bacteria)
KeywordsTRANSFERASE / PDH / ODH / acetyltransferase / lipoamide / corynebacterium / CoA / BCKDH / acyltransferase / mycobacterium / tuberculosis

+
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