2RDS

Crystal Structure of PtlH with Fe/oxalylglycine and ent-1-deoxypentalenic acid bound

Summary for 2RDS

• Entry DOI: 10.2210/pdb2rds/pdb
• Related: 2RDN 2RDQ 2RDR
• Descriptor: 1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase, FE (III) ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: double stranded barrel helix, dioxygenase, oxidoreductase
• Biological source: Streptomyces avermitilis
• Total number of polymer chains: 1
• Total formula weight: 33074.43

Authors

You, Z.,Omura, S.,Ikeda, H.,Cane, D.E.,Jogl, G. (deposition date: 2007-09-24, release date: 2007-10-16, Last modification date: 2024-02-21)

Primary citation

You, Z.,Omura, S.,Ikeda, H.,Cane, D.E.,Jogl, G.
Crystal Structure of the Non-heme Iron Dioxygenase PtlH in Pentalenolactone Biosynthesis.
J.Biol.Chem., 282:36552-36560, 2007

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.

PubMed: 17942405
DOI: 10.1074/jbc.M706358200

Experimental method

X-RAY DIFFRACTION (1.65 Å)