PDBsum entry 2de4

Hydrolase

PDB id: 2de4

Contents

Protein chains

344 a.a. *

Ligands

ACT ×2

BPS ×2

Waters ×775

* Residue conservation analysis

PDB id:

2de4

Name:

Hydrolase

Title:

Crystal structure of dszb c27s mutant in complex with biphenyl-2- sulfinic acid

Structure:

Dibenzothiophene desulfurization enzyme b. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Rhodococcus sp.. Organism_taxid: 54064. Strain: igts8. Gene: dszb. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.169 R-free: 0.199

Authors:

W.C.Lee,T.Ohshiro,T.Matsubara,Y.Izumi,M.Tanokura

Key ref:

W.C.Lee et al. (2006). Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase. J Biol Chem, 281, 32534-32539. PubMed id: 16891315 DOI: 10.1074/jbc.M602974200

Date:

08-Feb-06 Release date: 01-Aug-06

Protein chains

P54997  (DSZB_RHOSG) -  2'-hydroxybiphenyl-2-sulfinate desulfinase from Rhodococcus sp. (strain ATCC 53968 / IGTS8)

Seq: 365 a.a.

Struc: 344 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.13.1.3 - 2'-hydroxybiphenyl-2-sulfinate desulfinase.
• Reaction: 2'-hydroxybiphenyl-2-sulfinate + H2O = biphenyl-2-ol + sulfite + H⁺

2'-hydroxybiphenyl-2-sulfinate (Bound ligand (Het Group name = BPS) matches with 93.75% similarity) + H2O = biphenyl-2-ol + sulfite + H(+)

• Cofactor: FMN

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

reference

DOI no: 10.1074/jbc.M602974200

J Biol Chem 281:32534-32539 (2006)

PubMed id: 16891315

Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase.

W.C.Lee, T.Ohshiro, T.Matsubara, Y.Izumi, M.Tanokura.

ABSTRACT

The desulfurization of dibenzothiophene in Rhodococcus erythropolis is catalyzed by two monooxygenases, DszA and DszC, and a desulfinase, DszB. In the last step of this pathway, DszB hydrolyzes 2'-hydroxybiphenyl-2-sulfinic acid into 2-hydroxybiphenyl and sulfite. We report on the crystal structures of DszB and an inactive mutant of DszB in complex with substrates at resolutions of 1.8A or better. The overall fold of DszB is similar to those of periplasmic substrate-binding proteins. In the substrate complexes, biphenyl rings of substrates are recognized by extensive hydrophobic interactions with the active site residues. Binding of substrates accompanies structural changes of the active site loops and recruits His(60) to the active site. The sulfinate group of bound substrates forms hydrogen bonds with side chains of Ser(27), His(60), and Arg(70), each of which is shown by site-directed mutagenesis to be essential for the activity. In our proposed reaction mechanism, Cys(27) functions as a nucleophile and seems to be activated by the sulfinate group of substrates, whereas His(60) and Arg(70) orient the syn orbital of sulfinate oxygen to the sulfhydryl hydrogen of Cys(27) and stabilize the negatively charged reaction intermediate. Cys, His, and Arg residues are conserved in putative proteins homologous to DszB, which are presumed to constitute a new family of desulfinases.

Selected figure(s)

Figure 3.
FIGURE 3. Specific interaction between active site residues and HBPS. A, stereo view of HBPS bound to the active site. HBPS binds the active site mainly by hydrophobic interactions. Hydrogen bonds are indicated by the dashed lines. HBPS and residues in hydrophobic contacts with HBPS are labeled. Color scheme of the ribbon model is as in Fig. 2B. B, stereo view of the hydrogen bond network at the sulfinate group of HBPS. Hydrogen bonds are depicted with the dashed lines.

Figure 4.
FIGURE 4. Proposed reaction mechanism of DszB. The phenyl-hydroxy moieties of substrates are omitted for clarity.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 32534-32539) copyright 2006.

Figures were selected by an automated process.