PDBsum entry 1vz5

Oxidoreductase

PDB id: 1vz5

Contents

Protein chains

254 a.a. *

Ligands

SIN ×4

Waters ×524

* Residue conservation analysis

PDB id:

1vz5

Name:

Oxidoreductase

Title:

Succinate complex of atsk

Structure:

Putative alkylsulfatase atsk. Chain: a, b, c, d. Other_details: atsk-succinate complex

Source:

Pseudomonas putida. Organism_taxid: 303. Strain: s-313

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.15Å R-factor: 0.196 R-free: 0.225

Authors:

I.Mueller,A.C.Stueckl,I.Uson,M.Kertesz

Key ref:

I.Müller et al. (2005). Succinate complex crystal structures of the alpha-ketoglutarate-dependent dioxygenase AtsK: steric aspects of enzyme self-hydroxylation. J Biol Chem, 280, 5716-5723. PubMed id: 15542595 DOI: 10.1074/jbc.M410840200

Date:

14-May-04 Release date: 15-Nov-04

Protein chains

Q9WWU5  (ATSK_PSEPU) -  Alpha-ketoglutarate-dependent sulfate ester dioxygenase from Pseudomonas putida

Seq: 301 a.a.

Struc: 254 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.11.77 - alkyl sulfatase.
• Reaction: a primary linear alkyl sulfate ester + 2-oxoglutarate + O2 = an aldehyde + sulfate + succinate + CO2 + H⁺

primary linear alkyl sulfate ester + 2-oxoglutarate + O2 = aldehyde + sulfate + succinate + CO2 (Bound ligand (Het Group name = SIN) corresponds exactly) + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M410840200

J Biol Chem 280:5716-5723 (2005)

PubMed id: 15542595

Succinate complex crystal structures of the alpha-ketoglutarate-dependent dioxygenase AtsK: steric aspects of enzyme self-hydroxylation.

I.Müller, C.Stückl, J.Wakeley, M.Kertesz, I.Usón.

ABSTRACT

The alkylsulfatase AtsK from Pseudomonas putida S-313 is a member of the non-heme iron(II)-alpha-ketoglutarate-dependent dioxygenase superfamily. In the initial step of their catalytic cycle, enzymes belonging to this widespread and versatile family coordinate molecular oxygen to the iron center in the active site. The subsequent decarboxylation of the cosubstrate alpha-ketoglutarate yields carbon dioxide, succinate, and a highly reactive ferryl (IV) species, which is required for substrate oxidation via a complex mechanism involving the transfer of radical species. Non-productive activation of oxygen may lead to harmful side reactions; therefore, such enzymes need an effective built-in protection mechanism. One of the ways of controlling undesired side reactions is the self-hydroxylation of an aromatic side chain, which leads to an irreversibly inactivated species. Here we describe the crystal structure of the alkylsulfatase AtsK in complexes with succinate and with Fe(II)/succinate. In the crystal structure of the AtsK-Fe(II)-succinate complex, the side chain of Tyr(168) is co-ordinated to the iron, suggesting that Tyr(168) is the target of enzyme self-hydroxylation. This is the first structural study of an Fe(II)-alpha-ketoglutarate-dependent dioxygenase that presents an aromatic side chain coordinated to the metal center, thus allowing structural insight into this protective mechanism of enzyme self-inactivation.

Selected figure(s)

Figure 1.
FIG. 1. Alternative pathways for the reaction of the protein complex with oxygen in presence and absence of substrate. In the first step of the catalytic mechanism of all non-heme iron(II)- KG dependent dioxygenases, iron and the cosubstrate KG coordinate to the protein. In the next step, the substrate molecule approaches the active site (on the left), thereby displacing a water molecule from the metal center and liberating a coordinatively unsaturated iron atom. This facilitates dioxygen binding in the next step. One oxygen atom of O[2] is transferred to the cosubstrate, yielding succinate and carbon dioxide as reaction products. The iron is thereby oxidized, and a ferryl Fe(IV)=O species is formed, which then hydroxylates the substrate via a radical intermediate. In the absence of substrate, coordination of a dioxygen molecule to the iron(II)· KG complex can take place (on the right). In a self-protecting mechanism, one possible reaction pathway of the ferryl species formed after the decarboxylation of the KG is the reaction with an amino acid side chain such as tryptophan or tyrosine, as shown for the KG-dependent dioxygenases TfdA, AlkB, or TauD. As an alternative to this self-hydroxylation mechanism, the ferryl intermediate could react with a second cosubstrate molecule.

Figure 5.
FIG. 5. Active site region of the H[2]O-succinate-AtsK complex (a) the Fe-succinate-AtsK complex (b). The amino acids Ala^80 and His81 and Tyr166-Ala^169 of formerly disordered loops participate in a hydrogen bond network in the iron-succinate-AtsK complex that differs from that observed in the succinate-AtsK complex. The new hydrogen bonds and the relocation of -sheet 4 result in the formation of a lid over the active site of the Fe-succinate-AtsK complex.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 5716-5723) copyright 2005.

Figures were selected by an automated process.