4UUA

Crystal structure of zebrafish Sirtuin 5 in complex with 3S-Z-amino- succinylated CPS1-peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1002/anie.201402679
  • Primary Citation of Related Structures:  

  • 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; howeve ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
A, B
275Danio rerioMutation(s): 0 
Gene Names: sirt5
EC: 3.5.1.-
Find proteins for Q6DHI5 (Danio rerio)
Go to UniProtKB:  Q6DHI5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CARBAMOYLPHOSPHATE SYNTHETASE I
D
9Homo sapiensMutation(s): 0 
Gene Names: CPS1
EC: 6.3.4.16
Find proteins for P31327 (Homo sapiens)
Go to Gene View: CPS1
Go to UniProtKB:  P31327
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NX6
Query on NX6

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Download CCD File 
D
N-[(benzyloxy)carbonyl]-L-aspartic acid
C12 H13 N O6
XYXYXSKSTZAEJW-VIFPVBQESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BEZ
Query on BEZ
D
NON-POLYMERC7 H6 O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.208 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 87.190α = 90.00
b = 87.190β = 90.00
c = 313.870γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Atomic model, Derived calculations, Other
  • Version 1.2: 2014-10-08
    Type: Database references