3ATY | pdb_00003aty

Crystal structure of TcOYE

• PDB DOI: https://doi.org/10.2210/pdb3ATY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-26 Released: 2011-05-04 
• Deposition Author(s): Yamaguchi, K., Okamoto, N., Tokuoka, K., Sugiyama, S., Uchiyama, N., Matsumura, H., Inaka, K., Urade, Y., Inoue, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.195 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Structural insight into the stereoselective production of PGF2(alpha) by Old Yellow Enzyme from Trypanosoma cruzi

Okamoto, N., Yamaguchi, K., Mizohata, E., Tokuoka, K., Uchiyama, N., Sugiyama, S., Matsumura, H., Inaka, K., Urade, Y., Inoue, T.

(2011) J Biochem 150: 563-568

• PubMed: 21840922 
• DOI: https://doi.org/10.1093/jb/mvr096
• Primary Citation Related Structures: 
  3ATY, 3ATZ


• PubMed Abstract: 
  

  Old yellow enzyme (OYE) is an NADPH oxidoreductase capable of reducing a variety of compounds. It contains flavin mononucleotide (FMN) as a prosthetic group. A ternary complex structure of OYE from Trypanosoma cruzi (TcOYE) with FMN and one of the substrates, p-hydroxybenzaldehyde, shows a striking movement around the active site upon binding of the substrate. From a structural comparison of other OYE complexed with 12-oxophytodienoate, we have constructed a complex structure with another substrate, prostaglandin H(2) (PGH(2)), to provide a proposed stereoselective reaction mechanism for the reduction of PGH(2) to prostaglandin F(2α) by TcOYE.

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Organizational Affiliation: 
• Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka, Suita, Japan.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.54 kDa 
• Atom Count: 6,723 
• Modeled Residue Count: 756 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin F2a synthase	A, B	379	Trypanosoma cruzi	Mutation(s): 0  Gene Names: TcPGFS
UniProt
Find proteins for Q8I6L9 (Trypanosoma cruzi) Explore Q8I6L9  Go to UniProtKB:  Q8I6L9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.195 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.291	α = 90
b = 78.791	β = 93.37
c = 78.797	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Yamaguchi, K., Okamoto, N., Tokuoka, K., Sugiyama, S., Uchiyama, N., Matsumura, H., Inaka, K., Urade, Y., Inoue, T.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-01
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations