9JJ4 | pdb_00009jj4

NADP-dependent oxidoreductase complexed with NADP and substrate 1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.264 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Literature

Structural Basis for Medium-Chain Dehydrogenase/Reductase-Catalyzed Reductive Cyclization in Polycyclic Tetramate Macrolactam Biosynthesis.

Xie, X.Li, F.Mu, Y.Lu, M.Luo, J.Wang, H.Shen, Y.Du, L.Zhu, D.Li, Y.

(2025) J Am Chem Soc 147: 19253-19261

  • DOI: https://doi.org/10.1021/jacs.5c04971
  • Primary Citation of Related Structures:  
    9JI7, 9JJ4, 9JLK, 9JLY, 9JM9, 9JML, 9JP8

  • PubMed Abstract: 

    Few enzymes are known to catalyze reductive cyclizations via nucleophile-mediated C-C bond formation. Medium-chain dehydrogenases/reductases (MDRs) typically function as dehydrogenases or reductases. However, a distinct subclass of MDRs involved in polycyclic tetramate macrolactam (PoTeM) biosynthesis catalyzes reductive cyclizations via hydride-mediated C-C bond formation. Here, we present the apo and substrate-bound structures of OX4 and CftD, two enzymes responsible for the third ring formation in PoTeMs biosynthesis. Structural and mutational analysis reveal a catalytic mechanism wherein OX4 initiates a NADPH-dependent 1,6-reduction, followed by cyclization to form the C11-C22 bond, water-mediated protonation of the C7-carbonyl oxygen, and a final tautomerization to produce the cyclized product. Precise substrate positioning and stabilization of the enolate intermediate by the conserved residue W260 are critical for catalysis. These findings represent the first structural and mechanistic understanding of this newly identified cyclase subgroup and offer promising new avenues for enzyme engineering and natural product biosynthesis.


  • Organizational Affiliation
    • State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, People's Republic of China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADP-dependent oxidoreductase
A, B
354Lysobacter enzymogenesMutation(s): 0 
Gene Names: GLE_3219
UniProt
Find proteins for C3PTT2 (Lysobacter enzymogenes)
Explore C3PTT2 
Go to UniProtKB:  C3PTT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3PTT2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.264 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.719α = 90
b = 87.719β = 90
c = 226.086γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82173702

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release