8Z54 image
Deposition Date 2024-04-18
Release Date 2024-10-09
Last Version Date 2024-10-09
Entry Detail
PDB ID:
8Z54
Keywords:
Title:
Crystal structure of human SIRT5 in complex with succinylated Prx1 fragment
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.45 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NAD-dependent protein deacylase sirtuin-5, mitochondrial
Gene (Uniprot):SIRT5
Chain IDs:A
Chain Length:274
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Peroxiredoxin-1 fragment
Gene (Uniprot):PRDX1
Chain IDs:B
Chain Length:9
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SLL B LYS modified residue
Primary Citation
SIRT5 mutants reveal the role of conserved asparagine and glutamine residues in the NAD + -binding pocket.
Febs Lett. 598 2269 2280 (2024)
PMID: 39031546 DOI: 10.1002/1873-3468.14961

Abstact

SIRT5, one of the mammalian sirtuins, specifically recognizes succinyl-lysine residues on proteins and catalyzes the desuccinylation reaction. In this study, we characterized SIRT5 mutants with hydrophobic amino acid substitutions at Q140 and N141, in addition to the catalytic residue H158, known as an active site residue, by the Michaelis-Menten analysis and X-ray crystallography. Kinetic analysis showed that the catalytic efficiency (kcat/Km) of the Q140L and N141V mutants decreased to 0.02 times and 0.0038 times that of the wild-type SIRT5, respectively, with the activity of the N141V mutant becoming comparable to that of the H158M mutant. Our findings indicate that N141 contributes significantly to the desuccinylation reaction.

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Primary Citation of related structures