4UTX

Crystal structure of zebrafish Sirtuin 5 in complex with 3-nitro- propionylated CPS1-peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    4UTN, 4UTR, 4UUA, 4UUB, 4UTV, 4UU7, 4UU8, 4UTX, 4UTZ

  • 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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIALA, B275Danio rerioMutation(s): 0 
Gene Names: sirt5, si:ch211-121a2.1
EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q6DHI5 (Danio rerio)
Explore Q6DHI5 
Go to UniProtKB:  Q6DHI5
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CARBAMOYLPHOSPHATE SYNTHETASE IC9Homo sapiensMutation(s): 1 
Gene Names: CPS1
EC: 6.3.4.16
Find proteins for P31327 (Homo sapiens)
Explore P31327 
Go to UniProtKB:  P31327
NIH Common Fund Data Resources
PHAROS  P31327
GTEx  ENSG00000021826
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
3NP
Query on 3NP
Download Ideal Coordinates CCD File 
C
3-NITROPROPANOIC ACID
C3 H5 N O4
WBLZUCOIBUDNBV-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.49α = 90
b = 87.49β = 90
c = 313.79γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references, Other