[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

TitleMolecular basis for acetyl-CoA production by ATP-citrate lyase.
Journal, issue, pagesNat Struct Mol Biol, Vol. 27, Issue 1, Page 33-41, Year 2020
Publish dateDec 23, 2019
AuthorsXuepeng Wei / Kollin Schultz / Gleb A Bazilevsky / Austin Vogt / Ronen Marmorstein /
PubMed AbstractATP-citrate lyase (ACLY) synthesizes cytosolic acetyl coenzyme A (acetyl-CoA), a fundamental cellular building block. Accordingly, aberrant ACLY activity is observed in many diseases. Here we report ...ATP-citrate lyase (ACLY) synthesizes cytosolic acetyl coenzyme A (acetyl-CoA), a fundamental cellular building block. Accordingly, aberrant ACLY activity is observed in many diseases. Here we report cryo-EM structures of human ACLY, alone or bound to substrates or products. ACLY forms a homotetramer with a rigid citrate synthase homology (CSH) module, flanked by four flexible acetyl-CoA synthetase homology (ASH) domains; CoA is bound at the CSH-ASH interface in mutually exclusive productive or unproductive conformations. The structure of a catalytic mutant of ACLY in the presence of ATP, citrate and CoA substrates reveals a phospho-citryl-CoA intermediate in the ASH domain. ACLY with acetyl-CoA and oxaloacetate products shows the products bound in the ASH domain, with an additional oxaloacetate in the CSH domain, which could function in ACLY autoinhibition. These structures, which are supported by biochemical and biophysical data, challenge previous proposals of the ACLY catalytic mechanism and suggest additional therapeutic possibilities for ACLY-associated metabolic disorders.
External linksNat Struct Mol Biol / PubMed:31873304 / PubMed Central
MethodsEM (single particle)
Resolution2.85 - 4.3 Å
Structure data

20413

6poe

EMDB-20413, PDB-6poe:
Structure of ACLY in complex with CoA
Method: EM (single particle) / Resolution: 3.5 Å

20414

6pof

EMDB-20414, PDB-6pof:
Structure of human ATP citrate lyase
Method: EM (single particle) / Resolution: 4.3 Å

20783

6ui9

EMDB-20783, PDB-6ui9:
Structure of human ATP citrate lyase in complex with acetyl-CoA and oxaloacetate
Method: EM (single particle) / Resolution: 3.1 Å

20784

6uia

EMDB-20784, PDB-6uia:
Structure of ATP citrate lyase with CoA in a partially open conformation
Method: EM (single particle) / Resolution: 4.3 Å

20902

6uuw

EMDB-20902, PDB-6uuw:
Structure of human ATP citrate lyase E599Q mutant in complex with Mg2+, citrate, ATP and CoA
Method: EM (single particle) / Resolution: 2.85 Å

20903

6uuz

EMDB-20903, PDB-6uuz:
Structure of ACLY in the presence of citrate and CoA
Method: EM (single particle) / Resolution: 3.0 Å

20904

6uv5

EMDB-20904, PDB-6uv5:
Structure of human ATP citrate lyase in complex with acetyl-CoA and oxaloacetate
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-COA:
COENZYME A

ChemComp-HOH:
WATER

ChemComp-ACO:
ACETYL COENZYME *A

ChemComp-OAA:
OXALOACETATE ION

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-Y2A:
(2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy)ethyl]butanedioic acid


ChemComp, No image

ChemComp-UNL:
Unknown ligand

Source
  • homo sapiens (human)
KeywordsLYASE / apo / open conformation / enzyme

+
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://pdbjlvh1.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