PDBsum entry 1lnh

Oxidoreductase

PDB id

1lnh

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Contents

			Protein chain

					836 a.a. *

			Metals

					FE2

			Waters ×170

* Residue conservation analysis

PDB id:

1lnh

Links

Name:

Oxidoreductase

Title:

Lipoxygenase-3(soybean) non-heme fe(ii) metalloprotein

Structure:

Lipoxygenase-3. Chain: a

Source:

Glycine max. Soybean. Organism_taxid: 3847. Strain: provar cultivar

Resolution:

2.60Å

R-factor:

0.174

R-free:

0.265

Authors:

E.Skrzypczak-Jankun

Key ref:

E.Skrzypczak-Jankun et al. (1997). Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme. Proteins, 29, 15-31. PubMed id: 9294864

Date:

29-Mar-96

Release date:

02-Feb-97

PROCHECK

	Headers

	References

Protein chain

P09186 (LOX3_SOYBN) - Seed linoleate 9S-lipoxygenase-3 from Glycine max

Seq: Struc:

Seq: Struc:					857 a.a. 836 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 7 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.1.13.11.58 - linoleate 9S-lipoxygenase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

(9Z,12Z)-octadecadienoate + O2 = (9S)-hydroperoxy-(10E,12Z)- octadecadienoate

(9Z,12Z)-octadecadienoate	+	O2	=	(9S)-hydroperoxy-(10E,12Z)- octadecadienoate

Cofactor:

Fe cation

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

Key reference

	Proteins 29:15-31 (1997)
PubMed id: 9294864

Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme.
E.Skrzypczak-Jankun, L.M.Amzel, B.A.Kroa, M.O.Funk.

ABSTRACT

Soybean lipoxygenase isoenzyme L3 represents a second example (after L1) of the X-ray structure (R = 17% at 2.6 A resolution) for a member of the large family of lipoxygenases. L1 and L3 have different characteristics in catalysis, although they share 72% sequence identity (the changes impact 255 amino acids) and similar folding (average C alpha rms deviation of 1 A). The critical nonheme iron site has the same features as for L1:3O and 3N in pseudo C3v orientation, with two oxygen atoms (from Asn713 and water) at a nonbinding distance. Asn713 and His518 are strategically located at the junction of three cavities connecting the iron site with the molecule surface. The most visible differences between L1 and L3 isoenzymes occur in and near these cavities, affecting their accessibility and volume. Among the L1/L3 substitutions Glu256/ Thr274, Tyr409/His429, and Ser747/Asp766 affect the salt bridges (L1: Glu256...His248 and Asp490...Arg707) that in L1 restrict the access to the iron site from two opposite directions. The L3 molecule has a passage going through the whole length of the helical domain, starting at the interface with the Nt-domain (near 25-27 and 254-278) and going to the opposite end of the Ct-domain (near 367, 749). The substrate binding and the role of His513, His266, His776 (and other residues nearby) are illustrated and discussed by using models of linoleic acid binding. These hypotheses provide a possible explanation for a stringent stereo-specificity of catalytic products in L1 (that produces predominantly 13-hydroperoxide) versus the lack of such specificity in L3 (that turns out a mixture of 9- and 13-hydroperoxides and their diastereoisomers).

Literature references that cite this PDB file's key reference

PubMed id

Reference

19683507

J.Rapp, S.Xu, A.M.Sharp, W.P.Griffith, Y.W.Kim, and M.O.Funk (2009).
EPR spectroscopy and electrospray ionization mass spectrometry reveal distinctive features of the iron site in leukocyte 12-lipoxygenase.

Arch Biochem Biophys, 490, 50-56.

19244215

M.W.Buczynski, D.S.Dumlao, and E.A.Dennis (2009).
Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology.

J Lipid Res, 50, 1015-1038.

18972057

C.Jacquot, C.M.McGinley, E.Plata, T.R.Holman, and W.A.van der Donk (2008).
Synthesis of 11-thialinoleic acid and 14-thialinoleic acid, inhibitors of soybean and human lipoxygenases.

Org Biomol Chem, 6, 4242-4252.

18787124

L.Li, Z.Chang, Z.Pan, Z.Q.Fu, and X.Wang (2008).
Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase.

Proc Natl Acad Sci U S A, 105, 13883-13888.

PDB codes:

3dam 3dan 3dbm

18658287

S.Horowitz Brown, R.Zarnowski, W.C.Sharpee, and N.P.Keller (2008).
Morphological transitions governed by density dependence and lipoxygenase activity in Aspergillus flavus.

Appl Environ Microbiol, 74, 5674-5685.

18007054

D.B.Neau, N.C.Gilbert, S.G.Bartlett, A.Dassey, and M.E.Newcomer (2007).
Improving protein crystal quality by selective removal of a Ca(2+)-dependent membrane-insertion loop.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 972-975.

16790932

E.Skrzypczak-Jankun, O.Y.Borbulevych, M.I.Zavodszky, M.R.Baranski, K.Padmanabhan, V.Petricek, and J.Jankun (2006).
Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution.

Acta Crystallogr D Biol Crystallogr, 62, 766-775.

PDB codes:

1rrh 1rrl

17029406

F.Wu, and B.J.Gaffney (2006).
Dynamic behavior of fatty acid spin labels within a binding site of soybean lipoxygenase-1.

Biochemistry, 45, 12510-12518.

16641090

M.Cristea, and E.H.Oliw (2006).
A G316A mutation of manganese lipoxygenase augments hydroperoxide isomerase activity: mechanism of biosynthesis of epoxyalcohols.

J Biol Chem, 281, 17612-17623.

16162493

M.L.Oldham, A.R.Brash, and M.E.Newcomer (2005).
Insights from the X-ray crystal structure of coral 8R-lipoxygenase: calcium activation via a C2-like domain and a structural basis of product chirality.

J Biol Chem, 280, 39545-39552.

PDB code:

2fnq

14993710

E.Skrzypczak-Jankun, O.Y.Borbulevych, and J.Jankun (2004).
Soybean lipoxygenase-3 in complex with 4-nitrocatechol.

Acta Crystallogr D Biol Crystallogr, 60, 613-615.

PDB code:

1no3

14705020

O.Y.Borbulevych, J.Jankun, S.H.Selman, and E.Skrzypczak-Jankun (2004).
Lipoxygenase interactions with natural flavonoid, quercetin, reveal a complex with protocatechuic acid in its X-ray structure at 2.1 A resolution.

Proteins, 54, 13-19.

PDB code:

1n8q

12047377

L.Hörnsten, C.Su, A.E.Osbourn, U.Hellman, and E.H.Oliw (2002).
Cloning of the manganese lipoxygenase gene reveals homology with the lipoxygenase gene family.

Eur J Biochem, 269, 2690-2697.

12004065

M.Walther, M.Anton, M.Wiedmann, R.Fletterick, and H.Kuhn (2002).
The N-terminal domain of the reticulocyte-type 15-lipoxygenase is not essential for enzymatic activity but contains determinants for membrane binding.

J Biol Chem, 277, 27360-27366.

11179969

R.K.Hughes, D.M.Lawson, A.R.Hornostaj, S.A.Fairhurst, and R.Casey (2001).
Mutagenesis and modelling of linoleate-binding to pea seed lipoxygenase.

Eur J Biochem, 268, 1030-1040.

10625675

M.Jisaka, R.B.Kim, W.E.Boeglin, and A.R.Brash (2000).
Identification of amino acid determinants of the positional specificity of mouse 8S-lipoxygenase and human 15S-lipoxygenase-2.

J Biol Chem, 275, 1287-1293.

10446122

A.R.Brash (1999).
Lipoxygenases: occurrence, functions, catalysis, and acquisition of substrate.

J Biol Chem, 274, 23679-23682.

16429610

C.R.Bowers, V.Storhaug, C.E.Webster, J.Bharatam, A.Cottone, R.Gianna, K.Betsey, and B.J.Gaffney (1999).
Exploring surfaces and cavities in lipoxygenase and other proteins by hyperpolarized xenon-129 NMR.

J Am Chem Soc, 121, 9370-9377.

10097186

E.Hornung, M.Walther, H.Kühn, and I.Feussner (1999).
Conversion of cucumber linoleate 13-lipoxygenase to a 9-lipoxygenating species by site-directed mutagenesis.

Proc Natl Acad Sci U S A, 96, 4192-4197.

10585402

E.Sudharshan, and A.G.Rao (1999).
Involvement of cysteine residues and domain interactions in the reversible unfolding of lipoxygenase-1.

J Biol Chem, 274, 35351-35358.

10497176

L.Hörnsten, C.Su, A.E.Osbourn, P.Garosi, U.Hellman, C.Wernstedt, and E.H.Oliw (1999).
Cloning of linoleate diol synthase reveals homology with prostaglandin H synthases.

J Biol Chem, 274, 28219-28224.

9582345

C.Su, and E.H.Oliw (1998).
Manganese lipoxygenase. Purification and characterization.

J Biol Chem, 273, 13072-13079.

9799493

K.Schwarz, S.Borngräber, M.Anton, and H.Kuhn (1998).
Probing the substrate alignment at the active site of 15-lipoxygenases by targeted substrate modification and site-directed mutagenesis. Evidence for an inverse substrate orientation.

Biochemistry, 37, 15327-15335.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.