2rdn

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2rdn.gif|left|200px]]<br /><applet load="2rdn" size="350" color="white" frame="true" align="right" spinBox="true"
+
[[Image:2rdn.gif|left|200px]]
-
caption="2rdn, resolution 1.350&Aring;" />
+
 
-
'''Crystal Structure of PtlH with AKG and ent-1PL bound'''<br />
+
{{Structure
 +
|PDB= 2rdn |SIZE=350|CAPTION= <scene name='initialview01'>2rdn</scene>, resolution 1.350&Aring;
 +
|SITE=
 +
|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=AKG:2-OXYGLUTARIC+ACID'>AKG</scene> and <scene name='pdbligand=1PL:(1S,3aS,5aR,8aS)-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylic acid'>1PL</scene>
 +
|ACTIVITY=
 +
|GENE= ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])
 +
}}
 +
 
 +
'''Crystal Structure of PtlH with AKG and ent-1PL bound'''
 +
 
==Overview==
==Overview==
Line 7: Line 16:
==About this Structure==
==About this Structure==
-
2RDN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis] with <scene name='pdbligand=FE:'>FE</scene>, <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=AKG:'>AKG</scene> and <scene name='pdbligand=1PL:'>1PL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDN OCA].
+
2RDN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDN OCA].
==Reference==
==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17942405 17942405]
+
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:[http://www.ncbi.nlm.nih.gov/pubmed/17942405 17942405]
[[Category: Single protein]]
[[Category: Single protein]]
[[Category: Streptomyces avermitilis]]
[[Category: Streptomyces avermitilis]]
Line 26: Line 35:
[[Category: oxidoreductase]]
[[Category: oxidoreductase]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:46:28 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:35:00 2008''

Revision as of 16:35, 20 March 2008

Image:2rdn.gif


PDB ID 2rdn

Drag the structure with the mouse to rotate
, resolution 1.350Å
Ligands: , , and
Gene: ptlH (Streptomyces avermitilis)
Coordinates: save as pdb, mmCIF, xml



Crystal Structure of PtlH with AKG and ent-1PL 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

2RDN 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

Page seeded by OCA on Thu Mar 20 18:35:00 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2rdn"
Personal tools