4UTV

Crystal structure of zebrafish Sirtuin 5 in complex with 3-phenyl- succinylated CPS1-peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Chemical Probing of the Human Sirtuin 5 Active Site Reveals its Substrate Acyl Specificity and Peptide-Based Inhibitors.

Roessler, C.Nowak, T.Pannek, M.Gertz, M.Nguyen, G.T.Scharfe, M.Born, I.Sippl, W.Steegborn, C.Schutkowski, M.

(2014) Angew Chem Int Ed Engl 53: 10728

  • DOI: https://doi.org/10.1002/anie.201402679
  • Primary Citation of Related Structures:  
    4UTN, 4UTR, 4UTV, 4UTX, 4UTZ, 4UU7, 4UU8, 4UUA, 4UUB

  • PubMed Abstract: 

    Sirtuins are NAD(+)-dependent deacetylases acting as sensors in metabolic pathways and stress response. In mammals there are seven isoforms. The mitochondrial sirtuin 5 is a weak deacetylase but a very efficient demalonylase and desuccinylase; however, its substrate acyl specificity has not been systematically analyzed. Herein, we investigated a carbamoyl phosphate synthetase 1 derived peptide substrate and modified the lysine side chain systematically to determine the acyl specificity of Sirt5. From that point we designed six potent peptide-based inhibitors that interact with the NAD(+) binding pocket. To characterize the interaction details causing the different substrate and inhibition properties we report several X-ray crystal structures of Sirt5 complexed with these peptides. Our results reveal the Sirt5 acyl selectivity and its molecular basis and enable the design of inhibitors for Sirt5.


  • Organizational Affiliation

    Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale (Germany).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
A, B
275Danio rerioMutation(s): 0 
EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for Q6DHI5 (Danio rerio)
Explore Q6DHI5 
Go to UniProtKB:  Q6DHI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DHI5
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CARBAMOYLPHOSPHATE SYNTHETASE I9Homo sapiensMutation(s): 1 
EC: 6.3.4.16
UniProt & NIH Common Fund Data Resources
Find proteins for P31327 (Homo sapiens)
Explore P31327 
Go to UniProtKB:  P31327
PHAROS:  P31327
GTEx:  ENSG00000021826 
Entity Groups  
UniProt GroupP31327
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
F [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
FSL
Query on FSL

Download Ideal Coordinates CCD File 
I [auth C](2R)-2-phenylbutanedioic acid
C10 H10 O4
LVFFZQQWIZURIO-MRVPVSSYSA-N
F9V
Query on F9V

Download Ideal Coordinates CCD File 
J [auth C](2S)-2-phenylbutanedioic acid
C10 H10 O4
LVFFZQQWIZURIO-QMMMGPOBSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.91α = 90
b = 88.91β = 90
c = 305.33γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2022-12-07
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description