5YTK

Crystal structure of SIRT3 bound to a leucylated AceCS2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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
  • Primary Citation of Related Structures:  
    5YTK

  • 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 catalyzing the formation of lysine aminoacylation (K-AA) on its specific substrate proteins ...

    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. Electronic address: zhaosm@fudan.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A, B, C, D, E, F
A, B, C, D, E, F
274Homo sapiensMutation(s): 0 
Gene Names: SIRT3SIR2L3
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AceCS2-KLeuG,
H [auth J],
I [auth K],
J [auth L]
8Homo sapiensMutation(s): 0 
Gene Names: ACSS1ACAS2LKIAA1846
EC: 6.2.1.1 (UniProt), 6.2.1.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUB1 (Homo sapiens)
Explore Q9NUB1 
Go to UniProtKB:  Q9NUB1
PHAROS:  Q9NUB1
Entity Groups  
UniProt GroupQ9NUB1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download Ideal Coordinates CCD File 
N [auth B],
Q [auth C]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
LEU
Query on LEU

Download Ideal Coordinates CCD File 
M [auth B],
P [auth C],
U [auth G],
V [auth J],
W [auth K],
M [auth B],
P [auth C],
U [auth G],
V [auth J],
W [auth K],
X [auth L]
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
K [auth A],
L [auth B],
O [auth C],
R [auth D],
S [auth E],
K [auth A],
L [auth B],
O [auth C],
R [auth D],
S [auth E],
T [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.906α = 90
b = 108.906β = 90
c = 340.564γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report




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  (Full details and data files)

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