7CDH

Crystal structure of Betaaspartyl dipeptidase from thermophilic keratin degrading Fervidobacterium islandicum-AW-1

PDB DOI: https://doi.org/10.2210/pdb7CDH/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Fervidobacterium islandicum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-19 Released: 2020-12-30
Deposition Author(s): Dhanasingh, I., La, J.W., Lee, D.W., Lee, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.223
R-Value Work: 0.163
R-Value Observed: 0.166

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 33392259 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 43.39 kDa
Atom Count: 3,085
Modelled Residue Count: 367
Deposited Residue Count: 387
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoaspartyl dipeptidase	A [auth X]	387	Fervidobacterium islandicum	Mutation(s): 0 Gene Names: NA23_08080 EC: 3.4.19
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth X] SDF format, chain J [auth X] MOL2 format, chain H [auth X] MOL2 format, chain J [auth X] mmCIF format, chain H [auth X] mmCIF format, chain J [auth X]	H [auth X], J [auth X]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth X] Focus chain J [auth X] Interactions & Density Focus chain H [auth X] Focus chain J [auth X]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth X] SDF format, chain C [auth X] SDF format, chain D [auth X] SDF format, chain E [auth X] SDF format, chain F [auth X] SDF format, chain G [auth X] SDF format, chain I [auth X] MOL2 format, chain B [auth X] MOL2 format, chain C [auth X] MOL2 format, chain D [auth X] MOL2 format, chain E [auth X] MOL2 format, chain F [auth X] MOL2 format, chain G [auth X] MOL2 format, chain I [auth X] mmCIF format, chain B [auth X] mmCIF format, chain C [auth X] mmCIF format, chain D [auth X] mmCIF format, chain E [auth X] mmCIF format, chain F [auth X] mmCIF format, chain G [auth X] mmCIF format, chain I [auth X]	B [auth X] C [auth X] D [auth X] E [auth X] F [auth X] B [auth X], C [auth X], D [auth X], E [auth X], F [auth X], G [auth X], I [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain I [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain I [auth X]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth X] SDF format, chain L [auth X] MOL2 format, chain K [auth X] MOL2 format, chain L [auth X] mmCIF format, chain K [auth X] mmCIF format, chain L [auth X]	K [auth X], L [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth X] Focus chain L [auth X] Interactions & Density Focus chain K [auth X] Focus chain L [auth X]