3RIY

Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase

Du, J., Zhou, Y., Su, X., Yu, J.J., Khan, S., Jiang, H., Kim, J., Woo, J., Kim, J.H., Choi, B.H., He, B., Chen, W., Zhang, S., Cerione, R.A., Auwerx, J., Hao, Q., Lin, H.

(2011) Science 334: 806-809

  • DOI: 10.1126/science.1207861
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Silent information regulator 2 (Sir2) proteins (sirtuins) are nicotinamide adenine dinucleotide-dependent deacetylases that regulate important biological processes. Mammals have seven sirtuins, Sirt1 to Sirt7. Four of them (Sirt4 to Sirt7) have no de ...

    Silent information regulator 2 (Sir2) proteins (sirtuins) are nicotinamide adenine dinucleotide-dependent deacetylases that regulate important biological processes. Mammals have seven sirtuins, Sirt1 to Sirt7. Four of them (Sirt4 to Sirt7) have no detectable or very weak deacetylase activity. We found that Sirt5 is an efficient protein lysine desuccinylase and demalonylase in vitro. The preference for succinyl and malonyl groups was explained by the presence of an arginine residue (Arg(105)) and tyrosine residue (Tyr(102)) in the acyl pocket of Sirt5. Several mammalian proteins were identified with mass spectrometry to have succinyl or malonyl lysine modifications. Deletion of Sirt5 in mice appeared to increase the level of succinylation on carbamoyl phosphate synthase 1, which is a known target of Sirt5. Thus, protein lysine succinylation may represent a posttranslational modification that can be reversed by Sirt5 in vivo.

    Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent deacetylase sirtuin-5
A, B
273Homo sapiensMutation(s): 0 
Gene Names: SIRT5 (SIR2L5)
EC: 3.5.1.-
Find proteins for Q9NXA8 (Homo sapiens)
Go to Gene View: SIRT5
Go to UniProtKB:  Q9NXA8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide of histone 3 N-succinyl lysine 9
C, D
12Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to Gene View: HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J
Go to UniProtKB:  P68431
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD
Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SLL
Query on SLL
C, D
L-peptide linkingC10 H18 N2 O5LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.691α = 90.00
b = 69.417β = 90.00
c = 156.321γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-04-14 
  • Released Date: 2011-11-23 
  • Deposition Author(s): Zhou, Y., Hao, Q.

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2012-04-11
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description