4XRT | pdb_00004xrt

Crystal structure of the di-domain ARO/CYC StfQ from the steffimycin biosynthetic pathway

• PDB DOI: https://doi.org/10.2210/pdb4XRT/pdb

• Classification: LYASE
• Organism(s): Streptomyces steffisburgensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-21 Released: 2015-12-02 
• Deposition Author(s): Tsai, S.C., Caldara-Festin, G.M., Jackson, D.R., Aguilar, S., Patel, A., Nguyen, M., Sasaki, E., Valentic, T.R., Barajas, J.F., Vo, M., Khanna, A., Liu, H.-W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Structural and functional analysis of two di-domain aromatase/cyclases from type II polyketide synthases.

Caldara-Festin, G., Jackson, D.R., Barajas, J.F., Valentic, T.R., Patel, A.B., Aguilar, S., Nguyen, M., Vo, M., Khanna, A., Sasaki, E., Liu, H.W., Tsai, S.C.

(2015) Proc Natl Acad Sci U S A 112: E6844-E6851

• PubMed: 26631750 
• DOI: https://doi.org/10.1073/pnas.1512976112
• Primary Citation Related Structures: 
  4XRT, 4XRW


• PubMed Abstract: 
  

  Aromatic polyketides make up a large class of natural products with diverse bioactivity. During biosynthesis, linear poly-β-ketone intermediates are regiospecifically cyclized, yielding molecules with defined cyclization patterns that are crucial for polyketide bioactivity. The aromatase/cyclases (ARO/CYCs) are responsible for regiospecific cyclization of bacterial polyketides. The two most common cyclization patterns are C7-C12 and C9-C14 cyclizations. We have previously characterized three monodomain ARO/CYCs: ZhuI, TcmN, and WhiE. The last remaining uncharacterized class of ARO/CYCs is the di-domain ARO/CYCs, which catalyze C7-C12 cyclization and/or aromatization. Di-domain ARO/CYCs can further be separated into two subclasses: "nonreducing" ARO/CYCs, which act on nonreduced poly-β-ketones, and "reducing" ARO/CYCs, which act on cyclized C9 reduced poly-β-ketones. For years, the functional role of each domain in cyclization and aromatization for di-domain ARO/CYCs has remained a mystery. Here we present what is to our knowledge the first structural and functional analysis, along with an in-depth comparison, of the nonreducing (StfQ) and reducing (BexL) di-domain ARO/CYCs. This work completes the structural and functional characterization of mono- and di-domain ARO/CYCs in bacterial type II polyketide synthases and lays the groundwork for engineered biosynthesis of new bioactive polyketides.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697; Department of Chemistry, University of California, Irvine, CA 92697; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697;
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697; Department of Chemistry, University of California, Irvine, CA 92697; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697; [e-mail] [e-mail].
Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712; Department of Chemistry, University of Texas, Austin, TX 78712.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.32 kDa 
• Atom Count: 5,452 
• Modeled Residue Count: 601 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
StfQ Aromatase/Cyclase	A, B	329	Streptomyces steffisburgensis	Mutation(s): 0  Gene Names: stfQ
UniProt
Find proteins for Q2PA00 (Streptomyces steffisburgensis) Explore Q2PA00  Go to UniProtKB:  Q2PA00

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.976	α = 90
b = 92.433	β = 90
c = 138.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Tsai, S.C., Caldara-Festin, G.M., Jackson, D.R., Aguilar, S., Patel, A., Nguyen, M., Sasaki, E., Valentic, T.R., Barajas, J.F., Vo, M., Khanna, A., Liu, H.-W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3R01GM076330-04S1

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2015-12-30
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2024-02-28
  Changes: Data collection, Database references