PDBsum entry 2dki

Oxidoreductase

PDB id: 2dki

Contents

Protein chain

615 a.a. *

Ligands

SO4 ×3

FAD

Metals

_XE ×3

Waters ×380

* Residue conservation analysis

PDB id:

2dki

Name:

Oxidoreductase

Title:

Crystal structure of 3-hydroxybenzoate hydroxylase from comamonas testosteroni, under pressure of xenon gas (12 atm)

Structure:

3-hydroxybenzoate hydroxylase. Chain: a. Synonym: m-hydroxybenzoate hydroxylase. Ec: 1.14.13.23

Source:

Comamonas testosteroni. Organism_taxid: 285. Strain: kh122-3s

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.177 R-free: 0.236

Authors:

T.Hiromoto,S.Fujiwara,K.Hosokawa,H.Yamaguchi

Key ref:

T.Hiromoto et al. (2006). Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site. J Mol Biol, 364, 878-896. PubMed id: 17045293 DOI: 10.1016/j.jmb.2006.09.031

Date:

11-Apr-06 Release date: 24-Oct-06

Protein chain

Q6SSJ6  (MOBA_COMTE) -  3-hydroxybenzoate 4-monooxygenase from Comamonas testosteroni

Seq: 639 a.a.

Struc: 615 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.14.13.23 - 3-hydroxybenzoate 4-monooxygenase.
• Reaction: 3-hydroxybenzoate + NADPH + O2 + H⁺ = 3,4-dihydroxybenzoate + NADP⁺ + H2O
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

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

reference

DOI no: 10.1016/j.jmb.2006.09.031

J Mol Biol 364:878-896 (2006)

PubMed id: 17045293

Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site.

T.Hiromoto, S.Fujiwara, K.Hosokawa, H.Yamaguchi.

ABSTRACT

The 3-hydroxybenzoate hydroxylase (MHBH) from Comamonas testosteroni KH122-3s is a single-component flavoprotein monooxygenase, a member of the glutathione reductase (GR) family. It catalyzes the conversion of 3-hydroxybenzoate to 3,4-dihydroxybenzoate with concomitant requirements for equimolar amounts of NADPH and molecular oxygen. The production of dihydroxy-benzenoid derivative by hydroxylation is the first step in the aerobic degradation of various phenolic compounds in soil microorganisms. To establish the structural basis for substrate recognition, the crystal structure of MHBH in complex with its substrate was determined at 1.8 A resolution. The enzyme is shown to form a physiologically active homodimer with crystallographic 2-fold symmetry, in which each subunit consists of the first two domains comprising an active site and the C-terminal domain involved in oligomerization. The protein fold of the catalytic domains and the active-site architecture, including the FAD and substrate-binding sites, are similar to those of 4-hydroxybenzoate hydroxylase (PHBH) and phenol hydroxylase (PHHY), which are members of the GR family, providing evidence that the flavoprotein aromatic hydroxylases share similar catalytic actions for hydroxylation of the respective substrates. Structural comparison of MHBH with the homologous enzymes suggested that a large tunnel connecting the substrate-binding pocket to the protein surface serves for substrate transport in this enzyme. The internal space of the large tunnel is distinctly divided into hydrophilic and hydrophobic regions. The characteristically stratified environment in the tunnel interior and the size of the entrance would allow the enzyme to select its substrate by amphiphilic nature and molecular size. In addition, the structure of the Xe-derivative at 2.5 A resolution led to the identification of a putative oxygen-binding site adjacent to the substrate-binding pocket. The hydrophobic nature of the xenon-binding site extends to the solvent through the tunnel, suggesting that the tunnel could be involved in oxygen transport.

Selected figure(s)

Figure 4.
Figure 4. Stereo view of the FAD-binding site. The substrate and FAD molecules are shown as stick models, as in Figure 2(a). Residues around the FAD-binding site are shown as stick models and labeled. Water molecules are indicated as red spheres. The F[o]–F[c] omit electron-density map around the FAD molecule is colored cyan (countered at the 4.0 σ level).

Figure 6.
Figure 6. (a) Superposition of the C^α traces of MHBH and PHHY (PDB entry 1PN0).^18 MHBH and PHHY are colored blue and gray, respectively. Each molecule of 3-hydroxybenzoate and FAD in the MHBH structure is colored purple and yellow, respectively. For comparison with MHBH, the insertion segment of PHHY (residues 170–210) is shown in red. (b) The ribbon diagrams of: left, domain III (residues 453–639) of MHBH; and right, the human peroxiredoxin, hORF6 (PDB entry 1PRX).^45 Conserved cysteine residues, Cys521 in domain III and Cys47 located at the active site of hORF6, are shown as stick models.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 364, 878-896) copyright 2006.

Figures were selected by an automated process.