PDBsum entry 2v4j

Oxidoreductase

PDB id: 2v4j

Contents

Protein chains

436 a.a. *

380 a.a. *

103 a.a. *

Ligands

SF4 ×8

SH0 ×2

SRM-SO3 ×2

Waters ×1016

* Residue conservation analysis

PDB id:

2v4j

Name:

Oxidoreductase

Title:

The crystal structure of desulfovibrio vulgaris dissimilatory sulfite reductase bound to dsrc provides novel insights into the mechanism of sulfate respiration

Structure:

Sulfite reductase, dissimilatory-type subunit alpha. Chain: a, d. Synonym: dissimilatory sulfite reductase, desulfoviridin subunit alpha, hydrogensulfite reductase alpha subunit. Sulfite reductase, dissimilatory-type subunit beta. Chain: b, e. Synonym: dissimilatory sulfite reductase, desulfoviridin subunit beta, hydrogensulfite reductase subunit beta. Sulfite reductase, dissimilatory-type subunit gamma.

Source:

Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough. Atcc: 29579. Atcc: 29579

Resolution:

2.10Å R-factor: 0.192 R-free: 0.219

Authors:

T.F.Oliveira,C.Vonrhein,P.M.Matias,S.S.Venceslau,I.A.C.Pereira, M.Archer

Key ref:

T.F.Oliveira et al. (2008). The Crystal Structure of Desulfovibrio vulgaris Dissimilatory Sulfite Reductase Bound to DsrC Provides Novel Insights into the Mechanism of Sulfate Respiration. J Biol Chem, 283, 34141-34149. PubMed id: 18829451 DOI: 10.1074/jbc.M805643200

Date:

22-Sep-08 Release date: 02-Dec-08

Protein chains

P45574  (DSVA_DESVH) -  Sulfite reductase, dissimilatory-type subunit alpha from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)

Seq: 437 a.a.

Struc: 436 a.a.

Protein chains

P45575  (DSVB_DESVH) -  Sulfite reductase, dissimilatory-type subunit beta from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)

Seq: 381 a.a.

Struc: 380 a.a.

Protein chains

P45573  (DSVC_DESVH) -  Sulfite reductase, dissimilatory-type subunit gamma from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)

Seq: 105 a.a.

Struc: 103 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, D: E.C.1.8.99.3 - Transferred entry: 1.8.99.5.
• Reaction: (O₃S.S.SO(3))^2- + acceptor + 2 H₂O + OH^- = 3 HSO(3)^- + reduced acceptor
• Cofactor: Iron-sulfur; Siroheme

Iron-sulfur (Bound ligand (Het Group name = SH0) matches with 98.41% similarity) Siroheme

• Enzyme class 3: Chains B, C, E, F: E.C.1.8.1.22 - dissimilatory sulfite reductase.
• Reaction: [DsrC protein]-trisulfide + NAD⁺ + 3 H2O = [DsrC protein]-dithiol + sulfite + NADH + 3 H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.M805643200

J Biol Chem 283:34141-34149 (2008)

PubMed id: 18829451

The Crystal Structure of Desulfovibrio vulgaris Dissimilatory Sulfite Reductase Bound to DsrC Provides Novel Insights into the Mechanism of Sulfate Respiration.

T.F.Oliveira, C.Vonrhein, P.M.Matias, S.S.Venceslau, I.A.Pereira, M.Archer.

ABSTRACT

Sulfate reduction is one of the earliest types of energy metabolism used by ancestral organisms to sustain life. Despite extensive studies, many questions remain about the way respiratory sulfate reduction is associated with energy conservation. A crucial enzyme in this process is the dissimilatory sulfite reductase (dSiR), which contains a unique siroheme-[4Fe4S] coupled cofactor. Here, we report the structure of desulfoviridin from Desulfovibrio vulgaris, in which the dSiR DsrAB (sulfite reductase) subunits are bound to the DsrC protein. The alpha(2)beta(2)gamma(2) assembly contains two siroheme-[4Fe4S] cofactors bound by DsrB, two sirohydrochlorins and two [4Fe4S] centers bound by DsrA, and another four [4Fe4S] centers in the ferredoxin domains. A sulfite molecule, coordinating the siroheme, is found at the active site. The DsrC protein is bound in a cleft between DsrA and DsrB with its conserved C-terminal cysteine reaching the distal side of the siroheme. We propose a novel mechanism for the process of sulfite reduction involving DsrAB, DsrC, and the DsrMKJOP membrane complex (a membrane complex with putative disulfide/thiol reductase activity), in which two of the six electrons for reduction of sulfite derive from the membrane quinone pool. These results show that DsrC is involved in sulfite reduction, which changes the mechanism of sulfate respiration. This has important implications for models used to date ancient sulfur metabolism based on sulfur isotope fractionations.

Selected figure(s)

Figure 1.
Structure of the DsrAB sulfite reductase bound to DsrC. A, secondary structure representation of the α[2]β[2]γ[2] assembly (DsrAB sulfite reductase bound to DsrC), with the cofactors in ball-and-stick mode. DsrA (chains A and D) is colored blue, DsrB (chains B and E) is magenta, and DsrC (chains C and F) is green. The distance between the cofactors from one αβγ unit is displayed on the right side. Color code is yellow, carbon; red, oxygen; blue, nitrogen; brown, iron; and green, sulfur. B, molecular surface of theα[2]β[2]γ[2] assembly with oneαβγ unit in gray and the other colored according to A. C, superposition of DsrA and DsrB. N-term, N terminus; C-term, C terminus.

Figure 3.
Substrate and DsrC-binding channels. A, molecular surface of one αβγ unit showing the substrate channel, with a zoomed view of the channel entrance, containing a randomly placed ion for scale; the distal site of the siroheme (in yellow) is solvent-accessible. The color scheme is as in Fig. 1. B, surface representation of DsrAB with DsrC displaced from its binding position. The siroheme (in yellow) can be seen in the interior of the cleft formed between DsrAB. C, secondary structure view of one DsrABC unit with A. fulgidus DsrC (PDB code: 1SAU) superposed. The zoomed image shows the extended C-terminal arm of the D. vulgaris DsrC reaching the heme and the retracted arm from A. fulgidus DsrC. The two conserved cysteines of each DsrC are represented in stick mode, a dashed black line showing the close contact between Cys-103 and Cys-114 in A. fulgidus DsrC. Some water molecules at the interface are displayed as red spheres.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 34141-34149) copyright 2008.

Figures were selected by the author.