4UUB

Crystal structure of zebrafish Sirtuin 5 in complex with 2R-butyl- succinylated CPS1-peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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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
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
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CARBAMOYLPHOSPHATE SYNTHETASE IC [auth D]9Homo sapiensMutation(s): 1 
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 
G [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SU8
Query on SU8

Download Ideal Coordinates CCD File 
K [auth D](2R)-2-butylbutanedioic acid
C8 H14 O4
WOPLHDNLGYOSPG-ZCFIWIBFSA-N
DMS
Query on DMS

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

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

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.44α = 90
b = 87.44β = 90
c = 315.06γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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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, Other
  • Version 1.2: 2022-12-07
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description