8KEM | pdb_00008kem

PKS domains-fused AmpC EC2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 
    0.266 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.231 (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

Structural investigation of the docking domain assembly from trans-AT polyketide synthases.

Son, S.Y.Bae, D.W.Kim, E.Jeong, B.G.Kim, M.Y.Youn, S.Y.Yi, S.Kim, G.Hahn, J.S.Lee, N.K.Yoon, Y.J.Cha, S.S.

(2024) Structure 32: 1477-1487.e4

  • DOI: https://doi.org/10.1016/j.str.2024.05.017
  • Primary Citation Related Structures: 
    8KEM

  • PubMed Abstract: 

    Docking domains (DDs) located at the C- and N-termini of polypeptides play a crucial role in directing the assembly of polyketide synthases (PKSs), which are multienzyme complexes. Here, we determined the crystal structure of a complex comprising the C-terminal DD ( C DD MlnB ) and N-terminal DD ( N DD MlnC ) of macrolactin trans-acyltransferase (AT) PKS that were fused to a functional enzyme, AmpC EC2 β-lactamase. Interface analyses of the C DD MlnB / N DD MlnC complex revealed the molecular intricacies in the core section underpinning the precise DD assembly. Additionally, circular dichroism and steady-state kinetics demonstrated that the formation of the C DD MlnB / N DD MlnC complex had no influence on the structural and functional fidelity of the fusion partner, AmpC EC2. This inspired us to apply the C DD MlnB / N DD MlnC assembly to metabolon engineering. Indeed, DD assembly induced the formation of a complex between 4-coumarate-CoA ligase and chalcone synthase both involved in flavonoid biosynthesis, leading to a remarkable increase in naringenin production in vitro.


  • Organizational Affiliation
    • Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 142.11 kDa 
  • Atom Count: 9,464 
  • Modeled Residue Count: 1,248 
  • Deposited Residue Count: 1,284 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SDR family NAD(P)-dependent oxidoreductase,Beta-lactamase
A, B, C
428Bacillus amyloliquefaciensEscherichia coliMutation(s): 0 
Gene Names: RBAM_014350ampCRBAM_014340
EC: 3.5.2.6
UniProt
Find proteins for A7Z471 (Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42))
Explore A7Z471 
Go to UniProtKB:  A7Z471
Find proteins for A7Z472 (Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42))
Explore A7Z472 
Go to UniProtKB:  A7Z472
Find proteins for P00811 (Escherichia coli (strain K12))
Explore P00811 
Go to UniProtKB:  P00811
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00811A7Z472A7Z471
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.47α = 90
b = 248.86β = 90
c = 153.7γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Database references
  • Version 1.2: 2024-09-18
    Changes: Database references