3ATY

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195
R-Value Work: 0.170
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1093/jb/mvr096
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8I6L9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195
R-Value Work: 0.170
R-Value Observed: 0.170
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-05-04

Deposition Author(s):

Revision History (Full details and data files)

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