4OO2 | pdb_00004oo2

Streptomyces globisporus C-1027 FAD dependent (S)-3-chloro-β-tyrosine-S-SgcC2 C-5 hydroxylase SgcC apo form

• PDB DOI: https://doi.org/10.2210/pdb4OO2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces globisporus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-29 Released: 2014-02-12 
• Deposition Author(s): Cao, H., Xu, W., Bingman, C.A., Lohman, J.R., Yennamalli, R., Shen, B., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus.

Chang, C.Y., Lohman, J.R., Cao, H., Tan, K., Rudolf, J.D., Ma, M., Xu, W., Bingman, C.A., Yennamalli, R.M., Bigelow, L., Babnigg, G., Yan, X., Joachimiak, A., Phillips, G.N., Shen, B.

(2016) Biochemistry 55: 5142-5154

• PubMed: 27560143 
• DOI: https://doi.org/10.1021/acs.biochem.6b00713
• Primary Citation Related Structures: 
  4HX6, 4OO2, 4R82


• PubMed Abstract: 
  

  C-1027 is a chromoprotein enediyne antitumor antibiotic produced by Streptomyces globisporus. In the last step of biosynthesis of the (S)-3-chloro-5-hydroxy-β-tyrosine moiety of the C-1027 enediyne chromophore, SgcE6 and SgcC compose a two-component monooxygenase that hydroxylates the C-5 position of (S)-3-chloro-β-tyrosine. This two-component monooxygenase is remarkable for two reasons. (i) SgcE6 specifically reacts with FAD and NADH, and (ii) SgcC is active with only the peptidyl carrier protein (PCP)-tethered substrate. To address the molecular details of substrate specificity, we determined the crystal structures of SgcE6 and SgcC at 1.66 and 2.63 Å resolution, respectively. SgcE6 shares a similar β-barrel fold with the class I HpaC-like flavin reductases. A flexible loop near the active site of SgcE6 plays a role in FAD binding, likely by providing sufficient space to accommodate the AMP moiety of FAD, when compared to that of FMN-utilizing homologues. SgcC shows structural similarity to a few other known FADH2-dependent monooxygenases and sheds light on some biochemically but not structurally characterized homologues. The crystal structures reported here provide insights into substrate specificity, and comparison with homologues provides a catalytic mechanism of the two-component, FADH2-dependent monooxygenase (SgcE6 and SgcC) that catalyzes the hydroxylation of a PCP-tethered substrate.

---

Organizational Affiliation: 
• Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States.
BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States.
Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States.
Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.
Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology , Waknaghat, Himachal Pradesh, India 173234.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 235.72 kDa 
• Atom Count: 16,163 
• Modeled Residue Count: 2,023 
• Deposited Residue Count: 2,108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophenol-4-monooxygenase	A, B, C, D	527	Streptomyces globisporus	Mutation(s): 0  EC: 1.14.14.15
UniProt
Find proteins for Q8GMG6 (Streptomyces globisporus) Explore Q8GMG6  Go to UniProtKB:  Q8GMG6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A], G [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.156	α = 90
b = 173.729	β = 90
c = 113.859	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Cao, H., Xu, W., Bingman, C.A., Lohman, J.R., Yennamalli, R., Shen, B., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Structure summary
• Version 1.2: 2016-11-16
  Changes: Database references
• Version 1.3: 2016-12-07
  Changes: Structure summary
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2023-03-22
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-10-09
  Changes: Data collection, Structure summary