Biological Assembly 1  

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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: 74864.38 
• Atom Count: 5203 
• 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

• DOI: 10.2210/pdb1V3V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cavia porcellus
• Expression System: Escherichia coli BL21(DE3)


• 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 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:  
  1V3U, 1V3T


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase	A, B	333	Cavia porcellus	Mutation(s): 0  Gene Names: Ptgr1 (Ltb4dh) EC: 1.3.1.-
Find proteins for Q9EQZ5 (Cavia porcellus) Go to UniProtKB:  Q9EQZ5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NAP	A, B	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
5OP	A, B	(5E,13E)-11-HYDROXY-9,15-DIOXOPROSTA-5,13-DIEN-1-OIC ACID 15-OXO-PGE2 C20 H30 O5 YRTJDWROBKPZNV-SFTOQRQMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 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 = 90.00
b = 77.460	β = 102.29
c = 79.095	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
HKL-2000	data collection
CNS	refinement
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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance