6LJN

Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
ACE-HIS-PHE-SER-SLL5synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MCM
Query on MCM

Download Ideal Coordinates CCD File 
D [auth B]7-AMINO-4-METHYL-CHROMEN-2-ONE
C10 H9 N O2
GLNDAGDHSLMOKX-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SLL
Query on SLL
B
L-PEPTIDE LINKINGC10 H18 N2 O5LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.1α = 90
b = 55.403β = 90
c = 124.685γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 2.0: 2023-04-05
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description