Aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis

Experimental Data Snapshot

  • Resolution: 3.01 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis.

Petrova, T.E.Slutskaya, E.S.Boyko, K.M.Sokolova, O.S.Rakitina, T.V.Korzhenevskiy, D.A.Gorbacheva, M.A.Bezsudnova, E.Y.Popov, V.O.

(2015) Acta Crystallogr F Struct Biol Commun 71: 277-285

  • DOI: https://doi.org/10.1107/S2053230X15000783
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the aminopeptidase APDkam589 from the thermophilic crenarchaeon Desulfurococcus kamchatkensis was determined at a resolution of 3.0 Å. In the crystal, the monomer of APDkam589 and its symmetry-related monomers are densely packed to form a 12-subunit complex. Single-particle electron-microscopy analysis confirms that APDkam589 is present as a compact dodecamer in solution. The APDkam589 molecule is built similarly to the molecules of the PhTET peptidases, which have the highest sequence identity to APDkam589 among known structures and were isolated from the more thermostable archaeon Pyrococcus horikoshii. A comparison of the interactions of the subunits in APDkam589 with those in PhTET1, PhTET2 and PhTET3 reveals that APDkam589 has a much lower total number of salt bridges, which correlates with the lower thermostability of APDkam589. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. A superposition of the structure of APDkam589 with those having a high sequence similarity to APDkam589 reveals that, although the positions of Trp45, Trp252 and Trp358 are not conserved in the sequences, the spatial locations of the Trp residues in these models are similar.

  • Organizational Affiliation

    A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminopeptidase from family M42
A, B
394Desulfurococcus amylolyticus 1221nMutation(s): 1 
Gene Names: DKAM_0589
Find proteins for B8D484 (Desulfurococcus amylolyticus (strain DSM 18924 / JCM 16383 / VKM B-2413 / 1221n))
Explore B8D484 
Go to UniProtKB:  B8D484
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8D484
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.01 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 234.323α = 90
b = 234.323β = 90
c = 234.323γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2016-07-27
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description