PDBsum entry 1v3t

Oxidoreductase

PDB id: 1v3t

Contents

Protein chains

333 a.a. *

Ligands

NAP ×2

Waters ×814

* Residue conservation analysis

PDB id:

1v3t

Name:

Oxidoreductase

Title:

Crystal structure of leukotriene b4 12-hydroxydehydrogenase/15-oxo- prostaglandin 13-reductase

Structure:

Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15- keto reductase. Chain: a, b. Synonym: leukotriene b4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase. Engineered: yes

Source:

Cavia porcellus. Domestic guinea pig. Organism_taxid: 10141. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.194 R-free: 0.255

Authors:

T.Hori,T.Yokomizo,H.Ago,M.Sugahara,G.Ueno,M.Yamamoto,T.Kumasaka, T.Shimizu,M.Miyano,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Hori et al. (2004). Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop. J Biol Chem, 279, 22615-22623. PubMed id: 15007077 DOI: 10.1074/jbc.M312655200

Date:

05-Nov-03 Release date: 13-Jul-04

Protein chains

Q9EQZ5  (PTGR1_CAVPO) -  Prostaglandin reductase 1 from Cavia porcellus

Seq: 329 a.a.

Struc: 333 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.3.1.48 - 15-oxoprostaglandin 13-reductase.
• Reaction:
  1. 13,14-dihydro-15-oxo-prostaglandin E2 + NADP⁺ = 15-oxoprostaglandin E2 + NADPH + H⁺
  2. 13,14-dihydro-15-oxo-prostaglandin E2 + NAD⁺ = 15-oxoprostaglandin E2 + NADH + H⁺

13,14-dihydro-15-oxo-prostaglandin E2 + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = 15-oxoprostaglandin E2 + NADPH + H(+)

13,14-dihydro-15-oxo-prostaglandin E2 + NAD(+) (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) = 15-oxoprostaglandin E2 + NADH + H(+)

• Enzyme class 2: E.C.1.3.1.74 - 2-alkenal reductase [NAD(P)(+)].
• Reaction:
  1. an n-alkanal + NAD⁺ = an alk-2-enal + NADH + H⁺
  2. an n-alkanal + NADP⁺ = an alk-2-enal + NADPH + H⁺

n-alkanal + NAD(+) (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) = alk-2-enal + NADH + H(+)

n-alkanal + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = alk-2-enal + NADPH + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M312655200

J Biol Chem 279:22615-22623 (2004)

PubMed id: 15007077

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

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

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.

Selected figure(s)

Figure 3.
FIG. 3. NADP+ and 15-oxo-PGE[2] binding to LTB[4] 12-HD/PGR. A, a stereo view of the bound NADP+ in the binary complex structure. The|F[o]| -|F[c]| simulated annealing omit electron density map is contoured at 3.0 (orange) and 6.0 (cyan). The carbon atoms of NADP+ are yellow, and those of side chains involved in NADP+ binding are green. Single-letter codes are used for amino acid residues. The water molecules, oxygen, nitrogen, and phosphorus atoms are colored pink, red, blue, and orange, respectively. The hydrogen bonds are indicated by dashed lines. The main chain nitrogen or carbonyl groups interacting with the bound NADP+ are labeled by residue numbers. B, a photo of the ternary complex crystals (0.3 x 0.2 x 0.1 mm). C, absorption spectrum changes of a ternary complex solution mixture. A 1:10 dilution of the ternary mixture after NaOH addition was measured. D, stereo view of the -chain of bound 15-oxo-PGE[2] in the ternary complex structure. The carbon atoms of the -chain of 15-oxo-PGE[2] are colored in cyan, and NADP+ in yellow. The residues from the same subunit of the bound NADP+ around the -chain hydrophobic pore are colored in green, and those from the other subunit are in magenta.|F[o]| -|F[c]| simulated annealing omit electron density map is contoured at 2.4 (orange) and 3.5 (blue). The residues Ala-241, Tyr-245, and Met-248 are located on the loop E- F. Tyr-273 was refined as two conformers. E, a stereo view of the interaction between the -chain and NADP+. The hydrogen bonds and the - orbital interactions between the nicotine amide ring and the conjugated double bonds of the -chain are indicated in dashed lines. The shortest distance of the - orbital interactions is 3.2 Å between the carbonyl oxygen atom of 15-oxo-PGE[2] and the nitrogen atom of the nicotine amide ring.

Figure 5.
FIG. 5. Schematic drawing of the enolate anion intermediate in 15-oxo-PGE[2] reductase reaction mechanism. Only the -chain and the cyclopentane ring are represented (see "Results and Discussion" for further details).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 22615-22623) copyright 2004.

Figures were selected by the author.

Author's comment

The LTB[4] 12-HD/PGR inhibitor, indomethacin complex was reported. (Hori, T. et al., J Biochem (Tokyo). (2006, 140,457-66)).