7CF6

Crystal structure of Beta-aspartyl dipeptidase from thermophilic keratin degrading Fervidobacterium islandicum AW-1 in complex with beta-Asp-Leu dipeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Functional Characterization of Primordial Protein Repair Enzyme M38 Metallo-Peptidase From Fervidobacterium islandicum AW-1.

La, J.W.Dhanasingh, I.Jang, H.Lee, S.H.Lee, D.W.

(2020) Front Mol Biosci 7: 600634-600634

  • DOI: https://doi.org/10.3389/fmolb.2020.600634
  • Primary Citation of Related Structures:  
    7CDH, 7CF6

  • PubMed Abstract: 

    The NA23_RS08100 gene of Fervidobacterium islandicum AW-1 encodes a keratin-degrading β-aspartyl peptidase ( Fi BAP) that is highly expressed under starvation conditions. Herein, we expressed the gene in Escherichia coli , purified the recombinant enzyme to homogeneity, and investigated its function. The 318 kDa recombinant Fi BAP enzyme exhibited maximal activity at 80°C and pH 7.0 in the presence of Zn 2+ . Size-exclusion chromatography revealed that the native enzyme is an octamer comprising a tetramer of dimers; this was further supported by determination of its crystal structure at 2.6 Å resolution. Consistently, the structure of Fi BAP revealed three additional salt bridges in each dimer, involving 12 ionic interactions that might contribute to its high thermostability. In addition, the co-crystal structure containing the substrate analog N -carbobenzoxy-β-Asp-Leu at 2.7 Å resolution revealed binuclear Zn 2+ -mediated substrate binding, suggesting that Fi BAP is a hyperthermophilic type-I IadA, in accordance with sequence-based phylogenetic analysis. Indeed, complementation of a Leu auxotrophic E. coli mutant strain (Δ iadA and Δ leuB ) with Fi BAP enabled the mutant strain to grow on isoAsp-Leu peptides. Remarkably, LC-MS/MS analysis of soluble keratin hydrolysates revealed that Fi BAP not only cleaves the C-terminus of isoAsp residues but also has a relatively broad substrate specificity toward α-peptide bonds. Moreover, heat shock-induced protein aggregates retarded bacterial growth, but expression of BAP alleviated the growth defect by degrading damaged proteins. Taken together, these results suggest that the viability of hyperthermophiles under stressful conditions may rely on the activity of BAP within cellular protein repair systems.


  • Organizational Affiliation

    Department of Biotechnology, Yonsei University, Seoul, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoaspartyl dipeptidaseA [auth B],
B [auth A],
C,
D
391Fervidobacterium islandicumMutation(s): 0 
Gene Names: NA23_08080
EC: 3.4.19
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FWO (Subject of Investigation/LOI)
Query on FWO

Download Ideal Coordinates CCD File 
AA [auth D],
I [auth B],
P [auth A],
W [auth C]
(2S)-2-[[(3S)-3-azanyl-4-oxidanyl-4-oxidanylidene-butanoyl]amino]-4-methyl-pentanoic acid
C10 H18 N2 O5
IYJILWQAFPUBHP-BQBZGAKWSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
M [auth A],
T [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth B]
H [auth B]
L [auth A]
E [auth B],
F [auth B],
G [auth B],
H [auth B],
L [auth A],
N [auth A],
O [auth A],
S [auth C],
U [auth C],
V [auth C],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
J [auth B]
K [auth B]
Q [auth A]
BA [auth D],
CA [auth D],
J [auth B],
K [auth B],
Q [auth A],
R [auth A],
X [auth C],
Y [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: P 2 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.609α = 90
b = 150.425β = 90
c = 151.996γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description