5YTK

Crystal structure of SIRT3 bound to a leucylated AceCS2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sensing and Transmitting Intracellular Amino Acid Signals through Reversible Lysine Aminoacylations

He, X.D.Gong, W.Zhang, J.N.Nie, J.Yao, C.F.Guo, F.S.Lin, Y.Wu, X.H.Li, F.Li, J.Sun, W.C.Wang, E.D.An, Y.P.Tang, H.R.Yan, G.Q.Yang, P.Y.Wei, Y.Mao, Y.Z.Lin, P.C.Zhao, J.Y.Xu, Y.Xu, W.Zhao, S.M.

(2018) Cell Metab. 27: 151-166.e6

  • DOI: 10.1016/j.cmet.2017.10.015

  • PubMed Abstract: 
  • Amino acids are known regulators of cellular signaling and physiology, but how they are sensed intracellularly is not fully understood. Herein, we report that each aminoacyl-tRNA synthetase (ARS) senses its cognate amino acid sufficiency through cata ...

    Amino acids are known regulators of cellular signaling and physiology, but how they are sensed intracellularly is not fully understood. Herein, we report that each aminoacyl-tRNA synthetase (ARS) senses its cognate amino acid sufficiency through catalyzing the formation of lysine aminoacylation (K-AA) on its specific substrate proteins. At physiologic levels, amino acids promote ARSs bound to their substrates and form K-AAs on the ɛ-amine of lysines in their substrates by producing reactive aminoacyl adenylates. The K-AA marks can be removed by deacetylases, such as SIRT1 and SIRT3, employing the same mechanism as that involved in deacetylation. These dynamically regulated K-AAs transduce signals of their respective amino acids. Reversible leucylation on ras-related GTP-binding protein A/B regulates activity of the mammalian target of rapamycin complex 1. Glutaminylation on apoptosis signal-regulating kinase 1 suppresses apoptosis. We discovered non-canonical functions of ARSs and revealed systematic and functional amino acid sensing and signal transduction networks.


    Organizational Affiliation

    Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PRC; Key Laboratory of Reproduction Regulation of NPFPC (SIPPR,IRD) and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200032, PRC; State Key Laboratory of Biotherapy/ Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PRC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A, B, C, D, E, F
274Homo sapiensMutation(s): 0 
Gene Names: SIRT3 (SIR2L3)
EC: 3.5.1.-
Find proteins for Q9NTG7 (Homo sapiens)
Go to Gene View: SIRT3
Go to UniProtKB:  Q9NTG7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AceCS2-KLeu
G, J, K, L
8Homo sapiensMutation(s): 0 
Gene Names: ACSS1 (ACAS2L, KIAA1846)
EC: 6.2.1.1
Find proteins for Q9NUB1 (Homo sapiens)
Go to Gene View: ACSS1
Go to UniProtKB:  Q9NUB1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LEU
Query on LEU

Download SDF File 
Download CCD File 
B, C, G, J, K, L
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
LYS
Query on LYS

Download SDF File 
Download CCD File 
B, C
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.906α = 90.00
b = 108.906β = 90.00
c = 340.564γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-11-18 
  • Released Date: 2017-12-27 
  • Deposition Author(s): Li, J., Gong, W., Xu, Y.

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Database references