6NKI | pdb_00006nki

Structure of PhqB Reductase Domain from Penicillium fellutanum

• PDB DOI: https://doi.org/10.2210/pdb6NKI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Penicillium fellutanum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-07 Released: 2019-10-09 
• Deposition Author(s): Dan, Q., Newmister, S.A., Smith, J.L., Sherman, D.H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.325 (Depositor), 0.314 (DCC) 
• R-Value Work: 
  0.265 (Depositor), 0.276 (DCC) 
• R-Value Observed: 
  0.271 (Depositor) 

Literature

Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels-Alderase.

Dan, Q., Newmister, S.A., Klas, K.R., Fraley, A.E., McAfoos, T.J., Somoza, A.D., Sunderhaus, J.D., Ye, Y., Shende, V.V., Yu, F., Sanders, J.N., Brown, W.C., Zhao, L., Paton, R.S., Houk, K.N., Smith, J.L., Sherman, D.H., Williams, R.M.

(2019) Nat Chem 11: 972-980

• PubMed: 31548667 
• DOI: https://doi.org/10.1038/s41557-019-0326-6
• Primary Citation Related Structures: 
  6NKH, 6NKI, 6NKK, 6NKM


• PubMed Abstract: 
  

  Prenylated indole alkaloids such as the calmodulin-inhibitory malbrancheamides and anthelmintic paraherquamides possess great structural diversity and pharmaceutical utility. Here, we report complete elucidation of the malbrancheamide biosynthetic pathway accomplished through complementary approaches. These include a biomimetic total synthesis to access the natural alkaloid and biosynthetic intermediates in racemic form and in vitro enzymatic reconstitution to provide access to the natural antipode (+)-malbrancheamide. Reductive cleavage of an L-Pro-L-Trp dipeptide from the MalG non-ribosomal peptide synthetase (NRPS) followed by reverse prenylation and a cascade of post-NRPS reactions culminates in an intramolecular [4+2] hetero-Diels-Alder (IMDA) cyclization to furnish the bicyclo[2.2.2]diazaoctane scaffold. Enzymatic assembly of optically pure (+)-premalbrancheamide involves an unexpected zwitterionic intermediate where MalC catalyses enantioselective cycloaddition as a bifunctional NADPH-dependent reductase/Diels-Alderase. The crystal structures of substrate and product complexes together with site-directed mutagenesis and molecular dynamics simulations demonstrate how MalC and PhqE (its homologue from the paraherquamide pathway) catalyse diastereo- and enantioselective cyclization in the construction of this important class of secondary metabolites.

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Organizational Affiliation: 
• Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA. [e-mail].
Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA. [e-mail].
Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA. [e-mail].
Department of Chemistry, University of Michigan, Ann Arbor, MI, USA. [e-mail].
Department of Chemistry, Colorado State University, Fort Collins, CO, USA. [e-mail].
University of Colorado Cancer Center, Aurora, CO, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.09 kDa 
• Atom Count: 2,755 
• Modeled Residue Count: 356 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRPS	A	434	Penicillium fellutanum	Mutation(s): 0  Gene Names: phqB EC: 1 (UniProt), 6.3.1 (UniProt)
UniProt
Find proteins for L0E2U2 (Penicillium fellutanum) Explore L0E2U2  Go to UniProtKB:  L0E2U2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.325 (Depositor), 0.314 (DCC) 
• R-Value Work:  0.265 (Depositor), 0.276 (DCC) 
• R-Value Observed: 0.271 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.636	α = 90
b = 91.644	β = 90
c = 124.596	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Dan, Q., Newmister, S.A., Smith, J.L., Sherman, D.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA070375
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118101
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK042303

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references