› 6a9u

X-ray diffraction
2.4Å resolution

Crystal strcture of Icp55 from Saccharomyces cerevisiae bound to apstatin inhibitor

Released:
DOI: 10.2210/pdb6a9u/pdb
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PDB entry 6a9u coloured by chain, front view.
PDB entry 6a9u coloured by chain, side view.
PDB entry 6a9u coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function.
Singh R, Goyal VD, Kumar A, Sabharwal NS, Makde RD
FEBS Lett 593 443-454 (2019)
PMID: 30582634

Function and Biology Details

Reaction catalysed: 
The enzyme cleaves the 36-Pro-Pro-37 bond of cysteine desulfurase (EC 2.8.1.7) removing three amino acid residues (Tyr-Ser-Pro) from the N-terminus after cleavage by mitochondrial processing peptidase.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154013 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Intermediate cleaving peptidase 55 Chain: A
Molecule details ›
Chain: A
Length: 455 amino acids
Theoretical weight: 51.36 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P40051 (Residues: 58-511; Coverage: 89%)
Gene names: ICP55, YER078C
Sequence domains:
Structure domains: Creatinase/methionine aminopeptidase superfamily
apstatin Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 459 Da
Source organism: Polypodiopsida
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RRCAT INDUS-2 BEAMLINE PX-BL21
Spacegroup: I422
Unit cell:
a: 148.089Å b: 148.089Å c: 124.989Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.225 0.266
Expression systems:
  • Escherichia coli
  • Not provided

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Citations

1 citations in other articles

Genome-Wide Analysis of the Peptidase M24 Superfamily in Triticum aestivum Demonstrates That TaM24-9 Is Involved in Abiotic Stress Response.
Yan et al. (2022)

1 mention without citation

Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function.
Singh et al. (2019)

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