5ZK4 | pdb_00005zk4

The structure of DSZS acyltransferase with carrier protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.222 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural basis of protein-protein interactions between a trans-acting acyltransferase and acyl carrier protein in polyketide disorazole biosynthesis

Miyanaga, A.Ouchi, R.Ishikawa, F.Goto, E.Tanabe, G.Kudo, F.Eguchi, T.

(2018) J Am Chem Soc 140: 7970-7978

  • DOI: https://doi.org/10.1021/jacs.8b04162
  • Primary Citation Related Structures: 
    5ZK4

  • PubMed Abstract: 

    Acyltransferases (ATs) are responsible for the selection and incorporation of acyl building blocks in the biosynthesis of various polyketide natural products. The trans-AT modular polyketide synthases have a discrete trans-acting AT for the loading of an acyl unit onto the acyl carrier protein (ACP) located within each module. Despite the importance of protein-protein interactions between ATs and ACPs in trans-AT assembly lines, the dynamic actions of ACPs and trans-acting ATs remain largely uncharacterized because of the inherently transient nature of ACP-enzyme interactions. Herein, we report the crystal structure of the AT-ACP complex of disorazole trans-AT polyketide synthase. We used a bromoacetamide pantetheine cross-linking probe in combination with a Cys mutation to trap the transient AT-ACP complex, allowing the determination of the crystal structure of the disorazole AT-ACP complex at 2.03 Å resolution. On the basis of the cross-linked AT-ACP complex structure, ACP residues recognized by trans-acting AT were identified and validated by mutational studies, which demonstrated that the disorazole AT recognizes the loop 1 and helix III' residues of disorazole ACP. The disorazole AT-ACP complex structure presents a foundation for defining the dynamic processes associated with trans-acting ATs and provides detailed mechanistic insights into their ability to recognize ACPs.


  • Organizational Affiliation
    • Department of Chemistry , Tokyo Institute of Technology , 2-12-1, O-okayama , Meguro-ku, Tokyo 152-8551 , Japan.

Macromolecule Content 

  • Total Structure Weight: 88.67 kDa 
  • Atom Count: 5,939 
  • Modeled Residue Count: 720 
  • Deposited Residue Count: 792 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DisD protein
A, B
302Sorangium cellulosumMutation(s): 1 
Gene Names: dszDdisD
EC: 2.3.1.39
UniProt
Find proteins for Q4U443 (Sorangium cellulosum)
Explore Q4U443 
Go to UniProtKB:  Q4U443
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4U443
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DisA protein
C, D
94Sorangium cellulosumMutation(s): 0 
Gene Names: dszAdisA
UniProt
Find proteins for Q4U447 (Sorangium cellulosum)
Explore Q4U447 
Go to UniProtKB:  Q4U447
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4U447
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9EF

Query on 9EF



Download:Ideal Coordinates CCD File
I [auth A],
N [auth B]
N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
C13 H26 N3 O8 P
GTANJSAWPNEGPZ-NSHDSACASA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.222 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.324α = 90
b = 96.629β = 90
c = 99.056γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
ARP/wARPmodel building
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan17K07747

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary