Steric and conformational features of the aconitase mechanism

  title={Steric and conformational features of the aconitase mechanism},
  author={Hanspeter Lauble and Charles David Stout},
  journal={Proteins: Structure},
Crystal structures of mitochondrial aconitase with α‐methylisocitrate and with sulfate bound have been solved and refined at 2.0 Å resolution with R factors of 18.2 and 16.8%, respectively. The steric factors and conformational effects observed in both new structures support the proposed mechanism for the overall reaction catalyzed by aconitase. The alternate substrate α;methylisocitrate is derived from α;methyl‐cis‐aconitate during crystallization and is observed to bind in the active site in… 

Sites and mechanisms of aconitase inactivation by peroxynitrite: modulation by citrate and glutathione.

Aconitases are iron-sulfur cluster-containing proteins present both in mitochondria and cytosol of cells; the cubane iron-sulfur (Fe-S) cluster in the active site is essential for catalytic activity,

Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit.

Structural and kinetic results will help to engineer new stereospecific hydro-lyase enzymes for chemoenzymatic syntheses and reverse the evolution of HACN activity from an ancestral IPMI gene, demonstrating the evolutionary potential for promiscuity in hydro-LYase enzymes.

The environment of multinuclear copper metal linkages in protein structures

Abstract The extended environment, particularly of the second shell about multinuclear copper centers in protein tertiary structures, can be described in terms of polarity, hydrophobicity, secondary

The solution structure of apo-iron regulatory protein 1.

Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase.

It is reported that the isomerization of (2S,3S)-methylcitrate to (2R, 3S)-2-methylisocitrate requires a novel enzyme, methylcitrate dehydratase (PrpD), and the well-known enzyme, aconitase (AcnB), of the tricarboxylic acid cycle.

Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii.

The first structures of oxidized and reduced forms of the large subunit of IPM isomerase (ox- MJ0499 and red-MJ0499, respectively) from M. jannaschii are reported, helpful in understanding the biochemical mechanism of clustering of the Fe-S protein family.

A structural model for GroEL-polypeptide recognition.

  • A. BuckleR. ZahnA. Fersht
  • Chemistry, Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1997
A monomeric peptide fragment of GroEL, consisting of residues 191-376, is a mini-chaperone with a functional chaperoning activity that can explain many aspects of substrate binding and activity.

Folding and turnover of human iron regulatory protein 1 depend on its subcellular localization

The data show that proper folding of dual activity IRP1‐cytosolic aconitase is deficient in mitochondria, in contrast to genuine mitochondrial ac onitase, which emphasizes the role of molecular interactions in determining the fate of IRp1.

Conservation of aconitase residues revealed by multiple sequence analysis. Implications for structure/function relationships.

This work has aligned 28 members of the Fe-S isomerase family, identified highly conserved amino acid residues, and integrated this information with data on the crystallographic structure of mammalian mitochondrial aconitase to propose structural and/or functional roles for the previously unrecognized conserved residues.



Crystal structures of aconitase with trans-aconitate and nitrocitrate bound.

Comparison of the structures with isocitrate, trans-aconitate, nitrocitrate and sulfate bound reveals preferred orientations for the three types of oxygens ligated to Fe4 (carboxyl, hydroxyl and H2O) supporting the proposed roles for His101, Asp165 and His167 in the catalytic mechanism.

Crystal structures of aconitase with isocitrate and nitroisocitrate bound.

The crystal structures of mitochondrial aconitase with isocitrate and nitroisocitrate bound have been solved and refined to R factors of 0.179 and 0.161, respectively, for all observed data in the

Structure of activated aconitase: formation of the [4Fe-4S] cluster in the crystal.

  • A. RobbinsC. Stout
  • Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1989
The structure of activated pig heart aconitase [citrate(isocitrate) hydro-lyase, EC] containing a [4Fe-4S] cluster has been refined at 2.5-A resolution to a crystallographic residual of

Automated docking in crystallography: Analysis of the substrates of aconitase

The use of automated docking to explore the binding of substrates to aconitase and two binding modes of the catalytic intermediate cis‐aconitate correspond closely to the isocitrate and the citrate binding modes are proposed.

pH profiles and isotope effects for aconitases from Saccharomycopsis lipolytica, beef heart, and beef liver. alpha-Methyl-cis-aconitate and threo-Ds-alpha-methylisocitrate as substrates.

Data suggest a kinetic mechanism for beef aconitases in which product release occurs only by displacement by the substrate in a step independent of pH or of the protonation state of the substrate.

Characterization of the [4Fe-4S]+ cluster at the active site of aconitase by 57Fe, 33S, and 14N electron nuclear double resonance spectroscopy.

Methods devised by us for analyzing and simulating ENDOR spectra of a randomly oriented paramagnet have been used to determine the principal values and orientation relative to the g tensor for three of the four inequivalent iron sites of the [4Fe-4S]+ cluster, Fea, Feb2, and Feb3, in the substrate-free enzyme and the enzyme-substrate complex.

Engineering of protein bound iron‐sulfur clusters

An increasing number of iron-sulfur (Fe-S) proteins are found in which the Fe-S cluster is not involved in net electron transfer, as it is in the majority of Fe-S proteins. Most of the former are

Low-barrier hydrogen bonds and enzymic catalysis.

Several examples of enzymatic reactions that appear to use this principle are presented, and a weak hydrogen bond in the enzyme-substrate complex in which the pKa's do not match can become a strong, low-barrier one if the p Ka's become matched in the transition state or enzyme-intermediate complex.