2rdq
From Proteopedia
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|PDB= 2rdq |SIZE=350|CAPTION= <scene name='initialview01'>2rdq</scene>, resolution 1.310Å | |PDB= 2rdq |SIZE=350|CAPTION= <scene name='initialview01'>2rdq</scene>, resolution 1.310Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=AKG:2-OXYGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis]) | |GENE= ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2rdn|2RDN]], [[2rdr|2RDR]], [[2rds|2RDS]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdq OCA], [http://www.ebi.ac.uk/pdbsum/2rdq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2rdq RCSB]</span> | ||
}} | }} | ||
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[[Category: Omura, S.]] | [[Category: Omura, S.]] | ||
[[Category: You, Z.]] | [[Category: You, Z.]] | ||
| - | [[Category: AKG]] | ||
| - | [[Category: FE]] | ||
| - | [[Category: MG]] | ||
[[Category: dioxygenase]] | [[Category: dioxygenase]] | ||
[[Category: double stranded barrel helix]] | [[Category: double stranded barrel helix]] | ||
[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:59:12 2008'' |
Revision as of 01:59, 31 March 2008
| |||||||
| , resolution 1.310Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | ptlH (Streptomyces avermitilis) | ||||||
| Related: | 2RDN, 2RDR, 2RDS
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of PtlH with Fe/alpha ketoglutarate bound
Overview
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.
About this Structure
2RDQ is a Single protein structure of sequence from Streptomyces avermitilis. Full crystallographic information is available from OCA.
Reference
Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis., You Z, Omura S, Ikeda H, Cane DE, Jogl G, J Biol Chem. 2007 Dec 14;282(50):36552-60. Epub 2007 Oct 16. PMID:17942405
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