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 
  • R-Value Observed: 0.146 

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:  
    3RIG, 3RIY

  • 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 detectable or very weak deacetylase activity ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent deacetylase sirtuin-5A, B273Homo sapiensMutation(s): 0 
Gene Names: SIR2L5, SIRT5
EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q9NXA8 (Homo sapiens)
Explore Q9NXA8 
Go to UniProtKB:  Q9NXA8
NIH Common Fund Data Resources
PHAROS:  Q9NXA8
GTEx:  ENSG00000124523
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptide of histone 3 N-succinyl lysine 9C, D12N/AMutation(s): 0 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS:  P68431
GTEx:  ENSG00000197409ENSG00000197153ENSG00000278828ENSG00000275714ENSG00000273983ENSG00000274750ENSG00000275379ENSG00000277775
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
 F [auth A], H [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 E [auth A], G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SLL
Query on SLL		C, DL-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 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.691α = 90
b = 69.417β = 90
c = 156.321γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction

Structure Validation

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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  (Full details and data files)

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