6LJK

Crystal structure of human Sirt5 in complex with an internally quenched fluorescent substrate GluIQF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Sensitive fluorogenic substrates for sirtuin deacylase inhibitor discovery.

Yang, L.L.Wang, H.L.Yan, Y.H.Liu, S.Yu, Z.J.Huang, M.Y.Luo, Y.Zheng, X.Yu, Y.Li, G.B.

(2020) Eur J Med Chem 192: 112201-112201

  • DOI: https://doi.org/10.1016/j.ejmech.2020.112201
  • Primary Citation of Related Structures:  
    6LJK, 6LJM, 6LJN

  • PubMed Abstract: 

    Sirtuins (SIRTs) are NAD + -dependent lysine deacylases, regulating many important biological processes such as metabolism and stress responses. SIRT inhibitors may provide potential benefits against SIRT-driven human diseases. Development of efficient assay platforms based on fluorogenic substrates will facilitate the discovery of high-quality SIRT inhibitors. We here report 16 new fluorogenic peptide substrates (P1-P16) designed with structurally diverse tetrapeptides and acyl modifications. Tests of P1-P16 against SIRT isoforms identified several sensitive substrates for SIRT1, SIRT2, SIRT3 and SIRT5, which manifested lower K M values and higher catalytic efficiency, and particularly had less signal interference in inhibitor screening compared with our previously reported internally quenched fluorescent substrates. Co-crystallization of sensitive substrates P13 and P15 with SIRT5 revealed an unexpected binding mode, involving interactions with residues from active site bordering surfaces, different from that observed for other peptides derived from natural protein substrates. By using SIRT5 sensitive substrates, we found that TW-37, a Bcl-2 inhibitor, displayed low micromolar inhibition to SIRT5, which was further validated by isothermal titration calorimetry analyses, offering a new point to develop dual-action SIRT5/Bcl-2 inhibitors against cancers. This work provides assay platform and structural basis for developing new substrates and inhibitors targeting human SIRTs.


  • Organizational Affiliation

    College of Food and Bioengineering, Xihua University, Sichuan, 610039, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacylase sirtuin-5, mitochondrial272Homo sapiensMutation(s): 0 
Gene Names: SIRT5SIR2L5
EC: 2.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXA8 (Homo sapiens)
Explore Q9NXA8 
Go to UniProtKB:  Q9NXA8
PHAROS:  Q9NXA8
GTEx:  ENSG00000124523 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXA8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BE2-SER-ALA-ILE-LYS-SER-NIY-GLY-SET9synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
NIY
Query on NIY
B
L-PEPTIDE LINKINGC9 H10 N2 O5TYR
SET
Query on SET
B
L-PEPTIDE LINKINGC3 H8 N2 O2SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.997α = 90
b = 72.754β = 97.06
c = 55.876γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-11-22
    Changes: Refinement description