7Y8V | pdb_00007y8v

Crystal structure of AlbEF homolog mutant (AlbF-H54A/H58A) from Quasibacillus thermotolerans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.200 (Depositor) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the AlbEF complex involved in subtilosin A biosynthesis.

Ishida, K.Nakamura, A.Kojima, S.

(2022) Structure 30: 1637-1646.e3

  • DOI: https://doi.org/10.1016/j.str.2022.10.002
  • Primary Citation Related Structures: 
    7Y8U, 7Y8V, 7Y8X

  • PubMed Abstract: 

    Subtilosin A is a sactipeptide bacteriocin produced by Bacillus subtilis strain 168, containing intramolecular thioether bonds and a head-to-tail macrocyclic peptide bond. Macrocyclization is presumably catalyzed by AlbE and AlbF proteins encoded by the subtilosin A biosynthesis gene cluster. However, the underlying mechanism of macrocyclization remains uncertain as the tertiary structures of the proteins are undetermined. Here, we report the crystal structures of AlbE and AlbF homologs in Quasibacillus thermotolerans, wherein the subtilosin biosynthesis gene cluster is highly conserved. Structural analysis and pull-down assays revealed that AlbE and AlbF form heterodimeric complexes. Although the AlbEF complex shows structural similarity to M16B family metalloproteases, the substrate-binding chamber is shallower and more open than the other M16B family proteins. The chamber surface showed electrostatic complementarity to the precursor of subtilosin. Our findings provide insights into the role of AlbEF in metalloprotease catalysis and macrocyclic peptide bond formation.


  • Organizational Affiliation
    • Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.

Macromolecule Content 

  • Total Structure Weight: 89.35 kDa 
  • Atom Count: 6,007 
  • Modeled Residue Count: 717 
  • Deposited Residue Count: 761 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AlbE homologA [auth E]395Bacillus thermotoleransMutation(s): 0 
UniProt
Find proteins for A0A9X9ZA64 (Bacillus thermotolerans)
Explore A0A9X9ZA64 
Go to UniProtKB:  A0A9X9ZA64
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9X9ZA64
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AlbF homolog H54A/H58A mutantB [auth F]366Bacillus thermotoleransMutation(s): 2 
UniProt
Find proteins for A0A9X9ZA63 (Bacillus thermotolerans)
Explore A0A9X9ZA63 
Go to UniProtKB:  A0A9X9ZA63
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9X9ZA63
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth E]
D [auth E]
E
F [auth E]
H [auth F]
C [auth E],
D [auth E],
E,
F [auth E],
H [auth F],
I [auth F],
J [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth E]
K [auth F]
L [auth F]
M [auth F]
N [auth F]
G [auth E],
K [auth F],
L [auth F],
M [auth F],
N [auth F],
O [auth F],
P [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.200 (Depositor) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.423α = 90
b = 136.423β = 90
c = 119.001γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description