3LQY

Crystal structure of putative isochorismatase hydrolase from Oleispira antarctica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica.

Goral, A.M.Tkaczuk, K.L.Chruszcz, M.Kagan, O.Savchenko, A.Minor, W.

(2012) J Struct Funct Genomics 13: 27-36

  • DOI: 10.1007/s10969-012-9127-5
  • Primary Citation of Related Structures:  
    3LQY

  • PubMed 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 ...

    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).


    Related Citations: 
    • Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
      Kube, M., Chernikova, T.N., Al-Ramahi, Y., Beloqui, A., Lopez-Cortez, N., Guazzaroni, M.E., Heipieper, H.J., Klages, S., Kotsyurbenko, O.R., Langer, I., Nechitaylo, T.Y., Lunsdorf, H., Fernandez, M., Juarez, S., Ciordia, S., Singer, A., Kagan, O., Egorova, O., Petit, P.A., Stogios, P., Kim, Y., Tchigvintsev, A., Flick, R., Denaro, R., Genovese, M., Albar, J.P., Reva, O.N., Martinez-Gomariz, M., Tran, H., Ferrer, M., Savchenko, A., Yakunin, A.F., Yakimov, M.M., Golyshina, O.V., Reinhardt, R., Golyshin, P.N.
      (2013) Nat Commun 4: 2156

    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative isochorismatase hydrolaseA190Oleispira antarcticaMutation(s): 0 
Gene Names: OLEI00908_1_189
Find proteins for L7MTK1 (Oleispira antarctica)
Explore L7MTK1 
Go to UniProtKB:  L7MTK1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.59α = 90
b = 41.59β = 90
c = 171.198γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
CCP4model building
ARP/wARPmodel building
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-01-09
    Changes: Database references
  • Version 1.3: 2013-12-25
    Changes: Database references