8G7W

Type I modPKS reducing region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of a modular polyketide synthase reducing region.

McCullough, T.M.Dhar, A.Akey, D.L.Konwerski, J.R.Sherman, D.H.Smith, J.L.

(2023) Structure 31: 1109-1120.e3

  • DOI: https://doi.org/10.1016/j.str.2023.05.019
  • Primary Citation of Related Structures:  
    8G7W, 8G7X

  • PubMed Abstract: 

    The chemical scaffolds of numerous therapeutics are polyketide natural products, many formed by bacterial modular polyketide synthases (PKS). The large and flexible dimeric PKS modules have distinct extension and reducing regions. Structures are known for all individual enzyme domains and several extension regions. Here, we report the structure of the full reducing region from a modular PKS, the ketoreductase (KR), dehydratase (DH), and enoylreductase (ER) domains of module 5 of the juvenimicin PKS. The modular PKS-reducing region has a different architecture than the homologous fatty acid synthase (FAS) and iterative PKS systems in its arrangement of domains and dimer interface. The structure reveals a critical role for linker peptides in the domain interfaces, leading to discovery of key differences in KR domains dependent on module composition. Finally, our studies provide insight into the mechanism underlying modular PKS intermediate shuttling by carrier protein (ACP) domains.


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type I PKS module 4, module 5
A, B
1,067Micromonospora chalcea subsp. izumensisMutation(s): 0 
Gene Names: juvEIII
UniProt
Find proteins for A0A1Z1MZ77 (Micromonospora chalcea subsp. izumensis)
Explore A0A1Z1MZ77 
Go to UniProtKB:  A0A1Z1MZ77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z1MZ77
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.48α = 90
b = 204.48β = 90
c = 251.85γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
ISOLDErefinement
REFMACrefinement
PHENIXphasing
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01-DK042303
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30-GM138396
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118101

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references