PDBsum entry 2nwb

Oxidoreductase

PDB id: 2nwb

Contents

Protein chains

379 a.a. *

Ligands

HEM

Waters ×307

* Residue conservation analysis

PDB id:

2nwb

Name:

Oxidoreductase

Title:

Crystal structure of a putative 2,3-dioxygenase (so4414) from shewanella oneidensis in complex with ferric heme. Northeast structural genomics target sor52.

Structure:

Conserved domain protein. Chain: a, b. Synonym: putative 2,3-dioxygenase. Engineered: yes

Source:

Shewanella oneidensis. Organism_taxid: 211586. Strain: mr-1. Gene: so_4414. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.217 R-free: 0.225

Authors:

F.Forouhar,J.L.R.Anderson,C.G.Mowat,A.Hussain,J.Seetharaman, C.Bruckmann,S.J.Thackray,N.Khan,K.Cunningham,H.Janjua,L.Zhao,R.Xiao, L.C.Ma,J.Liu,M.C.Baran,T.B.Acton,B.Rost,G.T.Montelione,S.K.Champman, L.Tong,Northeast Structural Genomics Consortium (Nesg)

Key ref:

F.Forouhar et al. (2007). Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase. Proc Natl Acad Sci U S A, 104, 473-478. PubMed id: 17197414 DOI: 10.1073/pnas.0610007104

Date:

14-Nov-06 Release date: 19-Dec-06

Protein chains

Q8E972  (Q8E972_SHEON) -  Tryptophan 2,3-dioxygenase KynA from Shewanella oneidensis (strain MR-1)

Seq: 392 a.a.

Struc: 379 a.a.

Enzyme reactions

• Enzyme class: E.C.1.13.11.11 - tryptophan 2,3-dioxygenase.
• Pathway: Tryptophan Catabolism
• Reaction: L-tryptophan + O2 = N-formyl-L-kynurenine
• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

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

reference

DOI no: 10.1073/pnas.0610007104

Proc Natl Acad Sci U S A 104:473-478 (2007)

PubMed id: 17197414

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase.

F.Forouhar, J.L.Anderson, C.G.Mowat, S.M.Vorobiev, A.Hussain, M.Abashidze, C.Bruckmann, S.J.Thackray, J.Seetharaman, T.Tucker, R.Xiao, L.C.Ma, L.Zhao, T.B.Acton, G.T.Montelione, S.K.Chapman, L.Tong.

ABSTRACT

Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. Here, we report extensive structural and biochemical studies of the Xanthomonas campestris TDO and a related protein SO4414 from Shewanella oneidensis, including the structure at 1.6-A resolution of the catalytically active, ferrous form of TDO in a binary complex with the substrate L-Trp. The carboxylate and ammonium moieties of tryptophan are recognized by electrostatic and hydrogen-bonding interactions with the enzyme and a propionate group of the heme, thus defining the L-stereospecificity. A second, possibly allosteric, L-Trp-binding site is present at the tetramer interface. The sixth coordination site of the heme-iron is vacant, providing a dioxygen-binding site that would also involve interactions with the ammonium moiety of L-Trp and the amide nitrogen of a glycine residue. The indole ring is positioned correctly for oxygenation at the C2 and C3 atoms. The active site is fully formed only in the binary complex, and biochemical experiments confirm this induced-fit behavior of the enzyme. The active site is completely devoid of water during catalysis, which is supported by our electrochemical studies showing significant stabilization of the enzyme upon substrate binding.

Selected figure(s)

Figure 2.
Fig. 2. The structure of TDO. (a) Schematic representation of the structure of the monomer of X. campestris TDO. The -helices are shown in yellow and labeled. Heme is shown in gray, and L-Trp is shown in orange (labeled W). The water molecule is shown as a red sphere (labeled wat). (b) Schematic representation of the tetramer of X. campestris TDO. The four monomers are colored in yellow, cyan, violet, and green. Helices in the tetramer interface are labeled. The Trp molecules in the tetramer interface are also shown. Produced with Molscript (35) and rendered with Raster3D (36).

Figure 3.
Fig. 3. Molecular basis for substrate recognition by TDO. (a) Final 2F[o]–F[c] electron density at 1.6-Å resolution for heme, L-Trp, and a water in the active site. Contoured at 1 . (b) Stereo drawing showing the active site of X. campestris TDO in the binary complex with L-Trp. The segment in cyan is from another monomer of the tetramer. Hydrogen-bonding interactions are indicated with dashed lines in magenta. (c) Overlay of the structures of the free enzyme (in orchid) and the binary complex (yellow and cyan) in the active-site region. Regions of conformational differences are indicated with the red arrows. (d) Overlay of the active-site region of the second monomer (in green) and that of the first monomer (in yellow). Only the side-chain atoms of Trp are shown in the second monomer (in magenta). (e) Final 2F[o]–F[c] electron density at 1.6-Å resolution for heme, L-Trp, and a water in the active site of the second TDO molecule in the crystal. Contoured at 1 . Two conformations for the main chain atoms are shown, but neither fit the density well. For the stereo version of c and d, please see SI Fig. 7. Produced with Molscript (35) and rendered with Raster3D (36).

Figures were selected by an automated process.