8Z54

Crystal structure of human SIRT5 in complex with succinylated Prx1 fragment

• PDB DOI: https://doi.org/10.2210/pdb8Z54/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-18 Released: 2024-10-09 
• Deposition Author(s): Yokoyama, T., Takayama, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.227 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

SIRT5 mutants reveal the role of conserved asparagine and glutamine residues in the NAD + -binding pocket.

Yokoyama, T., Takayama, Y., Mizuguchi, M., Nabeshima, Y., Kusaka, K.

(2024) FEBS Lett 598: 2269-2280

• PubMed: 39031546 
• DOI: https://doi.org/10.1002/1873-3468.14961
• Primary Citation of Related Structures:  
  8Z54, 8Z55, 8Z56, 8Z57, 8Z58


• PubMed Abstract: 
  

  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 (k _cat /K _m ) 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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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, University of Toyama, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 31.48 kDa 
• Atom Count: 2,320 
• Modelled Residue Count: 271 
• Deposited Residue Count: 283 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	274	Homo sapiens	Mutation(s): 0  Gene Names: SIRT5, SIR2L5 EC: 2.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXA8 (Homo sapiens) Explore Q9NXA8  Go to UniProtKB:  Q9NXA8
PHAROS:  Q9NXA8 GTEx:  ENSG00000124523

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-1 fragment	B	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q06830 (Homo sapiens) Explore Q06830  Go to UniProtKB:  Q06830
PHAROS:  Q06830 GTEx:  ENSG00000117450

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SLL	B	L-PEPTIDE LINKING	C10 H18 N2 O5		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.227 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.202	α = 90
b = 72.612	β = 90
c = 162.407	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Yokoyama, T., Takayama, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release