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 

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.Genom. 13: 27-36

  • DOI: 10.1007/s10969-012-9127-5

  • 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 the ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
putative isochorismatase hydrolase
A
190Oleispira antarcticaMutation(s): 0 
Find proteins for L7MTK1 (Oleispira antarctica)
Go to UniProtKB:  L7MTK1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 41.590α = 90.00
b = 41.590β = 90.00
c = 171.198γ = 120.00
Software Package:
Software NamePurpose
HKL-3000phasing
REFMACrefinement
DMphasing
Cootmodel building
RESOLVEmodel building
HKL-2000data reduction
HKL-3000data collection
SHELXDphasing
SOLVEphasing
CCP4phasing
CCP4model building
ARP/wARPmodel building
HKL-2000data scaling
MLPHAREphasing
SHELXEmodel building
RESOLVEphasing
DMmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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