Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica

  • Anna M. Goral
  • Karolina L. Tkaczuk
  • Maksymilian Chruszcz
  • Olga Kagan
  • Alexei Savchenko
  • Wladek Minor
Article

Abstract

Isochorismatase-like hydrolases (IHL) constitute a large family of enzymes divided into five structural families (by SCOP). IHLs are crucial for siderophore-mediated ferric iron acquisition by cells. Knowledge of the structural characteristics of these molecules will enhance the understanding of the molecular basis of iron transport, and perhaps resolve which of the mechanisms previously proposed in the literature is the correct one. We determined the crystal structure of the apo-form of a putative isochorismatase hydrolase OaIHL (PDB code: 3LQY) from the antarctic γ-proteobacterium Oleispira antarctica, and did comparative sequential and structural analysis of its closest homologs. The characteristic features of all analyzed structures were identified and discussed. We also docked isochorismate to the determined crystal structure by in silico methods, to highlight the interactions of the active center with the substrate. The putative isochorismate hydrolase OaIHL from O. antarctica possesses the typical catalytic triad for IHL proteins. Its active center resembles those IHLs with a D–K–C catalytic triad, rather than those variants with a D–K–X triad. OaIHL shares some structural and sequential features with other members of the IHL superfamily. In silico docking results showed that despite small differences in active site composition, isochorismate binds to in the structure of OaIHL in a similar mode to its binding in phenazine biosynthesis protein PhzD (PDB code 1NF8).

Keywords

Iron uptake Isochorismatase hydrolases Structural comparison of isochorismatases Structural genomics 

Abbreviations

OaIHL

Putative isochorismatase hydrolase from Oleispira antarctica

IHL

Isochorismatase-like hydrolase

ISC

Isochorismate/isochorismic acid

Å

Angstrom

SCOP

Structural classification of proteins

PDB

Protein Data Bank

RMSD

Root mean square deviation

MSA

Multiple sequence alignment

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Anna M. Goral
    • 1
    • 3
    • 4
    • 5
  • Karolina L. Tkaczuk
    • 1
    • 3
  • Maksymilian Chruszcz
    • 1
    • 3
  • Olga Kagan
    • 2
    • 3
  • Alexei Savchenko
    • 2
    • 3
  • Wladek Minor
    • 1
    • 3
  1. 1.Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleUSA
  2. 2.Banting and Best Department of Medical ResearchUniversity of TorontoTorontoCanada
  3. 3.Midwest Center for Structural Genomics
  4. 4.Inter-Faculty Interdisciplinary Doctoral Studies in Natural Sciences and MathematicsUniversity of WarsawWarsawPoland
  5. 5.Faculty of ChemistryUniversity of WarsawWarsawPoland

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