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› 4utz

X-ray diffraction
3.3Å resolution

Crystal structure of zebrafish Sirtuin 5 in complex with adipoylated CPS1-peptide

Released:
DOI: 10.2210/pdb4utz/pdb
Model geometry
Fit model/data
PDB entry 4utz coloured by chain, front view.
PDB entry 4utz coloured by chain, side view.
PDB entry 4utz coloured by chain, top view.
Source organisms:
Primary publication:
Chemical probing of the human sirtuin 5 active site reveals its substrate acyl specificity and peptide-based inhibitors.
Roessler C, Nowak T, Pannek M, Gertz M, Nguyen GT, Scharfe M, Born I, Sippl W, Steegborn C, Schutkowski M
Angew Chem Int Ed Engl 53 10728-32 (2014)
PMID: 25111069

Function and Biology Details

Reaction catalysed: 
hydrogencarbonate + NH4(+) + 2 ATP = carbamoyl phosphate + 2 ADP +phosphate + 2 H(+).
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179516 (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 BL21(DE3)
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: D
Molecule details ›
Chain: D
Length: 9 amino acids
Theoretical weight: 969 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P31327 (Residues: 524-531; Coverage: 1%)
Gene name: CPS1

Ligands and Environments

6 bound ligands:
Ligand ZN 2 x ZN
Ligand EPE 1 x EPE
Ligand DMS 1 x DMS
Ligand NA 1 x NA
Ligand EDO 1 x EDO
Ligand 0L1 1 x 0L1
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P6522
Unit cell:
a: 87.32Å b: 87.32Å c: 314.57Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.209 0.254
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

12 review citations

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