Crystal Structure of PtlH with Fe/alpha ketoglutarate bound

Experimental Data Snapshot

  • Resolution: 1.31 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Crystal Structure of the Non-heme Iron Dioxygenase PtlH in Pentalenolactone Biosynthesis.

You, Z.Omura, S.Ikeda, H.Cane, D.E.Jogl, G.

(2007) J Biol Chem 282: 36552-36560

  • DOI: https://doi.org/10.1074/jbc.M706358200
  • Primary Citation of Related Structures:  
    2RDN, 2RDQ, 2RDR, 2RDS

  • PubMed Abstract: 

    The non-heme iron dioxygenase PtlH from the soil organism Streptomyces avermitilis is a member of the iron(II)/alpha-ketoglutarate-dependent dioxygenase superfamily and catalyzes an essential reaction in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. To investigate the structural basis for substrate recognition and catalysis, we have determined the x-ray crystal structure of PtlH in several complexes with the cofactors iron, alpha-ketoglutarate, and the non-reactive enantiomer of the substrate, ent-1-deoxypentalenic acid, in four different crystal forms to up to 1.31 A resolution. The overall structure of PtlH forms a double-stranded barrel helix fold, and the cofactor-binding site for iron and alpha-ketoglutarate is similar to other double-stranded barrel helix fold enzymes. Additional secondary structure elements that contribute to the substrate-binding site in PtlH are not conserved in other double-stranded barrel helix fold enzymes. Binding of the substrate enantiomer induces a reorganization of the monoclinic crystal lattice leading to a disorder-order transition of a C-terminal alpha-helix. The newly formed helix blocks the major access to the active site and effectively traps the bound substrate. Kinetic analysis of wild type and site-directed mutant proteins confirms a critical function of two arginine residues in substrate binding, while simulated docking of the enzymatic reaction product reveals the likely orientation of bound substrate.

  • Organizational Affiliation

    Department of Chemistry, Brown University, Providence, Rhode Island 02912-9108, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase288Streptomyces avermitilisMutation(s): 0 
Gene Names: ptlH
Find proteins for Q82IZ1 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680))
Explore Q82IZ1 
Go to UniProtKB:  Q82IZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82IZ1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.31 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.817α = 90
b = 70.869β = 98.21
c = 48.769γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations