PDBsum entry 1fgm

Go to PDB code: 
protein metals links
Oxidoreductase PDB id
Protein chain
818 a.a. *
Waters ×681
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Lipoxygenase-1 (soybean) at 100k, n694h mutant
Structure: Seed lipoxygenase-1. Chain: a. Synonym: l-1. Engineered: yes. Mutation: yes
Source: Glycine max. Soybean. Organism_taxid: 3847. Expressed in: escherichia coli. Expression_system_taxid: 562
1.90Å     R-factor:   0.178     R-free:   0.212
Authors: D.R.Tomchick,W.Minor,T.R.Holman
Key ref:
D.R.Tomchick et al. (2001). Structural and functional characterization of second-coordination sphere mutants of soybean lipoxygenase-1. Biochemistry, 40, 7509-7517. PubMed id: 11412104
28-Jul-00     Release date:   24-Oct-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P08170  (LOX1_SOYBN) -  Seed linoleate 13S-lipoxygenase-1
839 a.a.
818 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Linoleate 13S-lipoxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
1. Linoleate + O2 = (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate
2. Alpha-linolenate + O2 = (9Z,11E,13S,15Z)-13-hydroperoxyoctadeca- 9,11,15-trienoate
+ O(2)
= (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate
+ O(2)
= (9Z,11E,13S,15Z)-13-hydroperoxyoctadeca- 9,11,15-trienoate
      Cofactor: Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  


Biochemistry 40:7509-7517 (2001)
PubMed id: 11412104  
Structural and functional characterization of second-coordination sphere mutants of soybean lipoxygenase-1.
D.R.Tomchick, P.Phan, M.Cymborowski, W.Minor, T.R.Holman.
Lipoxygenases are an important class of non-heme iron enzymes that catalyze the hydroperoxidation of unsaturated fatty acids. The details of the enzymatic mechanism of lipoxygenases are still not well understood. This study utilizes a combination of kinetic and structural probes to relate the lipoxygenase mechanism of action with structural modifications of the iron's second coordination sphere. The second coordination sphere consists of Gln(495) and Gln(697), which form a hydrogen bond network between the substrate cavity and the first coordination sphere (Asn(694)). In this investigation, we compared the kinetic and structural properties of four mutants (Q495E, Q495A, Q697N, and Q697E) with those of wild-type soybean lipoxygenase-1 and determined that changes in the second coordination sphere affected the enzymatic activity by hydrogen bond rearrangement and substrate positioning through interaction with Gln(495). The nature of the C-H bond cleavage event remained unchanged, which demonstrates that the mutations have not affected the mechanism of hydrogen atom tunneling. The unusual and dramatic inverse solvent isotope effect (SIE) observed for the Q697E mutant indicated that an Fe(III)-OH(-) is the active site base. A new transition state model for hydrogen atom abstraction is proposed.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20422083 F.Mei, C.Ou, G.Wu, L.Cao, F.Han, X.Meng, J.Li, D.Li, and Z.Liao (2010).
Non-heme iron(II/III) complexes that model the reactivity of lipoxygenase with a redox switch.
  Dalton Trans, 39, 4267-4269.  
19645454 A.T.Wecksler, V.Kenyon, N.K.Garcia, J.D.Deschamps, W.A.van der Donk, and T.R.Holman (2009).
Kinetic and structural investigations of the allosteric site in human epithelial 15-lipoxygenase-2.
  Biochemistry, 48, 8721-8730.  
18685763 L.Cuesta, E.Tomat, V.M.Lynch, and J.L.Sessler (2008).
Binuclear organometallic ruthenium complexes of a Schiff base expanded porphyrin.
  Chem Commun (Camb), (), 3744-3746.  
18216254 M.P.Meyer, D.R.Tomchick, and J.P.Klinman (2008).
Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1.
  Proc Natl Acad Sci U S A, 105, 1146-1151.
PDB codes: 3bnb 3bnc 3bnd 3bne
18656914 R.Sarangi, R.K.Hocking, M.L.Neidig, M.Benfatto, T.R.Holman, E.I.Solomon, K.O.Hodgson, and B.Hedman (2008).
Geometric structure determination of N694C lipoxygenase: a comparative near-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure study.
  Inorg Chem, 47, 11543-11550.  
19061319 S.C.Sharma, and J.P.Klinman (2008).
Experimental evidence for hydrogen tunneling when the isotopic arrhenius prefactor (A(H)/A(D)) is unity.
  J Am Chem Soc, 130, 17632-17633.  
17274015 I.Tejero, A.González-Lafont, and J.M.Lluch (2007).
A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1.
  J Comput Chem, 28, 997.  
17523638 M.L.Neidig, A.T.Wecksler, G.Schenk, T.R.Holman, and E.I.Solomon (2007).
Kinetic and spectroscopic studies of N694C lipoxygenase: a probe of the substrate activation mechanism of a nonheme ferric enzyme.
  J Am Chem Soc, 129, 7531-7537.  
17385891 M.S.Rogers, E.M.Tyler, N.Akyumani, C.R.Kurtis, R.K.Spooner, S.E.Deacon, S.Tamber, S.J.Firbank, K.Mahmoud, P.F.Knowles, S.E.Phillips, M.J.McPherson, and D.M.Dooley (2007).
The stacking tryptophan of galactose oxidase: a second-coordination sphere residue that has profound effects on tyrosyl radical behavior and enzyme catalysis.
  Biochemistry, 46, 4606-4618.
PDB codes: 2eib 2eic 2eid 2eie
18003930 M.Y.Pau, J.D.Lipscomb, and E.I.Solomon (2007).
Substrate activation for O2 reactions by oxidized metal centers in biology.
  Proc Natl Acad Sci U S A, 104, 18355-18362.  
17022084 B.Youn, G.E.Sellhorn, R.J.Mirchel, B.J.Gaffney, H.D.Grimes, and C.Kang (2006).
Crystal structures of vegetative soybean lipoxygenase VLX-B and VLX-D, and comparisons with seed isoforms LOX-1 and LOX-3.
  Proteins, 65, 1008-1020.
PDB codes: 2iuj 2iuk
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.  
16628755 M.Schurink, W.J.van Berkel, H.J.Wichers, and C.G.Boeriu (2006).
Identification of lipoxygenase inhibitory peptides from beta-casein by using SPOT synthesis.
  Chembiochem, 7, 743-747.  
16157595 G.Coffa, A.N.Imber, B.C.Maguire, G.Laxmikanthan, C.Schneider, B.J.Gaffney, and A.R.Brash (2005).
On the relationships of substrate orientation, hydrogen abstraction, and product stereochemistry in single and double dioxygenations by soybean lipoxygenase-1 and its Ala542Gly mutant.
  J Biol Chem, 280, 38756-38766.  
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
  Chem Commun (Camb), (), 5843-5863.  
15357019 E.H.Oliw, M.Cristea, and M.Hamberg (2004).
Biosynthesis and isomerization of 11-hydroperoxylinoleates by manganese- and iron-dependent lipoxygenases.
  Lipids, 39, 319-323.  
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
12598659 E.I.Solomon, A.Decker, and N.Lehnert (2003).
Non-heme iron enzymes: contrasts to heme catalysis.
  Proc Natl Acad Sci U S A, 100, 3589-3594.  
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.  
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.