Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 74.86 kDa 
• Atom Count: 6148 
• Modelled Residue Count: 661 
• Deposited Residue Count: 666 
• Unique protein chains: 1

1V3V

Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complexed with NADP and 15-oxo-PGE2

• PDB DOI: 10.2210/pdb1V3V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cavia porcellus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-11-06 Released: 2004-07-13 
• Deposition Author(s): Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.194 

Literature

Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop

Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M.

(2004) J Biol Chem 279: 22615-22623

• PubMed: 15007077 
• DOI: 10.1074/jbc.M312655200
• Primary Citation of Related Structures:  
  1V3T, 1V3U, 1V3V


• PubMed Abstract: 
  

The bifunctional leukotriene B(4) 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase (LTB(4) 12-HD/PGR) is an essential enzyme for eicosanoid inactivation. It is involved in the metabolism of the E and F series of 15-oxo-prostaglandins (15-oxo-PGs), leukotriene B(4) (LTB(4)), and 15-oxo-lipoxin A(4) (15-oxo-LXA(4)). Some nonsteroidal anti-inflammatory drugs (NSAIDs), which primarily act as cyclooxygenase inhibitors also inhibit LTB(4) 12-HD/PGR activity. Here we report the crystal structure of the LTB(4) 12-HD/PGR, the binary complex structure with NADP(+), and the ternary complex structure with NADP(+) and 15-oxo-PGE(2). In the ternary complex, both in the crystalline form and in solution, the enolate anion intermediate accumulates as a brown chromophore. PGE(2) contains two chains, but only the omega-chain of 15-oxo-PGE(2) was defined in the electron density map in the ternary complex structure. The omega-chain was identified at the hydrophobic pore on the dimer interface. The structure showed that the 15-oxo group forms hydrogen bonds with the 2'-hydroxyl group of nicotine amide ribose of NADP(+) and a bound water molecule to stabilize the enolate intermediate during the reductase reaction. The electron-deficient C13 atom of the conjugated enolate may be directly attacked by a hydride from the NADPH nicotine amide in a stereospecific manner. The moderate recognition of 15-oxo-PGE(2) is consistent with a broad substrate specificity of LTB(4) 12-HD/PGR. The structure also implies that a Src homology domain 3 may interact with the left-handed proline-rich helix at the dimer interface and regulate LTB(4) 12-HD/PGR activity by disruption of the substrate binding pore to accommodate the omega-chain.

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Organizational Affiliation: 

Structural Biophysics Laboratory, Highthroughput Factory, Coherent X-ray Optics Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki, Sayo-gun, Hyogo 679-5148, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase	A, B	333	Cavia porcellus	Mutation(s): 0  Gene Names: Ptgr1, Ltb4dh EC: 1.3.1.48 (PDB Primary Data), 1.3.1.74 (UniProt)
UniProt
Find proteins for Q9EQZ5 (Cavia porcellus) Explore Q9EQZ5  Go to UniProtKB:  Q9EQZ5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	F [auth A], K [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
5OP	G [auth A], L [auth B]	(5E,13E)-11-HYDROXY-9,15-DIOXOPROSTA-5,13-DIEN-1-OIC ACID C20 H30 O5 YRTJDWROBKPZNV-SFTOQRQMSA-N
CL	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.553	α = 90
b = 77.46	β = 102.29
c = 79.095	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-06 
• Released Date: 2004-07-13 
Deposition Author(s): Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance