PDBsum entry 3bnc

Oxidoreductase

PDB id: 3bnc

Contents

Protein chain

823 a.a. *

Ligands

ACY

Metals

_FE

Waters ×801

* Residue conservation analysis

PDB id:

3bnc

Name:

Oxidoreductase

Title:

Lipoxygenase-1 (soybean) i553g mutant

Structure:

Seed lipoxygenase-1. Chain: a. Synonym: l-1. Engineered: yes. Mutation: yes

Source:

Glycine max. Soybean. Organism_taxid: 3847. Gene: lox1.1, lox1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.65Å R-factor: 0.170 R-free: 0.201

Authors:

D.R.Tomchick

Key ref:

M.P.Meyer et al. (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. PubMed id: 18216254 DOI: 10.1073/pnas.0710643105

Date:

14-Dec-07 Release date: 01-Apr-08

Protein chain

P08170  (LOX1_SOYBN) -  Seed linoleate 13S-lipoxygenase-1 from Glycine max

Seq: 839 a.a.

Struc: 823 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.13.11.12 - linoleate 13S-lipoxygenase.
• Reaction:
  1. (9Z,12Z)-octadecadienoate + O2 = (13S)-hydroperoxy-(9Z,11E)- octadecadienoate
  2. (9Z,12Z,15Z)-octadecatrienoate + O2 = (13S)-hydroperoxy-(9Z,11E,15Z)- octadecatrienoate
• Cofactor: Fe cation

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

Added reference

DOI no: 10.1073/pnas.0710643105

Proc Natl Acad Sci U S A 105:1146-1151 (2008)

PubMed id: 18216254

Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1.

M.P.Meyer, D.R.Tomchick, J.P.Klinman.

ABSTRACT

This study examines the impact of a series of mutations at position 553 on the kinetic and structural properties of soybean lipoxygenase-1 (SLO-1). The previously uncharacterized mutants reported herein are I553L, I553V, and I553G. High-resolution x-ray studies of these mutants, together with the earlier studied I553A, show almost no structural change in relation to the WT-enzyme. By contrast, a progression in kinetic behavior occurs in which the decrease in the size of the side chain at position 553 leads to an increased importance of donor-acceptor distance sampling in the course of the hydrogen transfer process. These dynamical changes in behavior are interpreted in the context of two general classes of protein motions, preorganization and reorganization, with the latter including the distance sampling modes [Klinman JP (2006) Philos Trans R Soc London Ser B 361:1323-1331; Nagel Z, Klinman JP (2006) Chem Rev 106:3095-3118]. The aggregate data for SLO-1 show how judicious placement of hydrophobic side chains can influence enzyme catalysis via enhanced donor-acceptor hydrogenic wave function overlap.

Selected figure(s)

Figure 4.
Configuration of ligands to the active site iron atom in I553L. The leucine side chain at position 546 resides one helix turn away, in the direction of the catalytically active iron center. The shadow at position 553 traces out the region occupied by isoleucine in the WT-SLO.

Figure 5.
Configuration of ligands to the active site iron atom in I553G. The leucine side chain at position 546 resides one helix turn away, in the direction of the catalytically active iron center. The shadow at position 553 traces out the region occupied by isoleucine in the WT-SLO.

Figures were selected by an automated process.