› 5ojo

X-ray diffraction
3.1Å resolution

Sirtuin 5 from Danio rerio in complex with 3-hydroxy-3-methylglutaryl-CPS1 peptide

Released:
DOI: 10.2210/pdb5ojo/pdb
PDB entry 5ojo coloured by chain, front view.
PDB entry 5ojo coloured by chain, side view.
PDB entry 5ojo coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.
Pannek M, Simic Z, Fuszard M, Meleshin M, Rotili D, Mai A, Schutkowski M, Steegborn C
OpenAccess logo Nat Commun 8 1513 (2017)
PMID: 29138502

Function and Biology Details

Reaction catalysed: 
(1a) ATP + HCO(3)(-) = ADP + carboxyphosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-151978 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacylase sirtuin-5, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 275 amino acids
Theoretical weight: 30.42 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6DHI5 (Residues: 30-298; Coverage: 88%)
Gene names: si:ch211-121a2.1, sirt5
Sequence domains: Sir2 family
Structure domains:
Carbamoyl-phosphate synthase [ammonia], mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 8 amino acids
Theoretical weight: 1.11 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P31327 (Residues: 525-531; Coverage: 1%)
Gene name: CPS1

Ligands and Environments

5 bound ligands:
Ligand DMS 1 x DMS
Ligand ZN 2 x ZN
Ligand EDO 1 x EDO
Ligand EPE 1 x EPE
Ligand NA 1 x NA
2 modified residues:
Ligand HLY 1 x HLY
Ligand SKH 1 x SKH

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P6522
Unit cell:
a: 87.54Å b: 87.54Å c: 316.92Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.196 0.266
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

23 review citations

Sirtuin activators and inhibitors: Promises, achievements, and challenges.
Dai et al. (2018)
22 more

1 mention without citation

Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.
Pannek et al. (2017)