3RIY image
Deposition Date 2011-04-14
Release Date 2011-11-23
Last Version Date 2023-11-01
Entry Detail
PDB ID:
3RIY
Keywords:
Title:
Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.55 Å
R-Value Free:
0.19
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NAD-dependent deacetylase sirtuin-5
Gene (Uniprot):SIRT5
Chain IDs:A, B
Chain Length:273
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:peptide of histone 3 N-succinyl lysine 9
Chain IDs:C, D
Chain Length:12
Number of Molecules:2
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SLL C LYS ?
Primary Citation
Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase
Science 334 806 809 (2011)
PMID: 22076378 DOI: 10.1126/science.1207861

Abstact

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.

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Primary Citation of related structures