PDBsum entry: 3ciw

Adomet binding protein

PDB id: 3ciw

Contents

Protein chain

347 a.a. *

Ligands

SF4-SAH

CPS ×5

SAT

Metals

_CL ×3

Waters ×426

* Residue conservation analysis

PDB id:

3ciw

Name:

Adomet binding protein

Title:

X-ray structure of the [fefe]-hydrogenase maturase hyde from thermotoga maritima

Structure:

Fefe-hydrogenase maturase. Chain: a. Engineered: yes

Source:

Thermotoga maritima. Gene: hyde. Expressed in: escherichia coli.

Resolution:

1.35Å R-factor: 0.145 R-free: 0.177

Authors:

Y.Nicolet,J.K.Ruback,M.C.Posewitz,P.Amara,C.Mathevon,M.Atta, M.Fontecave,J.C.Fontecilla-Camps

Key ref:

Y.Nicolet et al. (2008). X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima. J Biol Chem, 283, 18861-18872. PubMed id: 18400755 DOI: 10.1074/jbc.M801161200

Date:

12-Mar-08 Release date: 08-Apr-08

Protein chain

Q9X0Z6  (Q9X0Z6_THEMA) -  Biotin synthetase, putative

Seq: 348 a.a.

Struc: 347 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (4 terms)

DOI no: 10.1074/jbc.M801161200

J Biol Chem 283:18861-18872 (2008)

PubMed id: 18400755

X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima.

Y.Nicolet, J.K.Rubach, M.C.Posewitz, P.Amara, C.Mathevon, M.Atta, M.Fontecave, J.C.Fontecilla-Camps.

ABSTRACT

Maturation of the [FeFe]-hydrogenase active site depends on at least the expression of three gene products called HydE, HydF, and HydG. We have solved the high resolution structure of recombinant, reconstituted S-adenosine-L-methionine-dependent HydE from Thermotoga maritima. Besides the conserved [Fe(4)S(4)] cluster involved in the radical-based reaction, this HydE was reported to have a second [Fe(4)S(4)] cluster coordinated by three Cys residues. However, in our crystals, depending on the reconstitution and soaking conditions, this second cluster is either a [Fe(2)S(2)] center, with water occupying the fourth ligand site or is absent. We have carried out site-directed mutagenesis studies on the related HydE from Clostridium acetobutylicum, along with in silico docking and crystal soaking experiments, to define the active site region and three anion-binding sites inside a large, positive cavity, one of which binds SCN(-) with high affinity. Although the overall triose-phosphate isomerase-barrel structure of HydE is very similar to that of biotin synthase, the residues that line the internal cavity are significantly different in the two enzymes.

Selected figure(s)

Figure 2.
FIGURE 2. A, stereoview of the environment of AdoHCys in the active site. Water molecules are represented by red spheres. All hydrogen bonds with distances between 2.2 and 3.2 Å are depicted by purple dot lines. The corresponding distances are shown in Table 2. The 2F[o] - F[c] electron density map contoured at the 1 level is depicted as a blue grid. B, Leu^305 is represented in olive green or blue with either AdoMet or AdoHCys bound, respectively. Only AdoMet is depicted, because, except for the missing C , no significant differences are observed between AdoMet and AdoHCys positions.

Figure 5.
FIGURE 5. Active site cavity. A, stereo view of the substrate binding region. The purple dot corresponds to the 5' carbon atom where the radical will be initially located upon reduction. The large semitransparent brown sphere defines the putative substrate-binding site (or at least the location where radical transfer should occur), based on comparisons with E. coli BioB (43) and lysine 2,3-aminomutase (49). The remaining spheres correspond to the location of the carboxylate moieties (red) and partial positive charges (blue) deduced from the molecular docking experiment. The two disordered and partially occupied Cl^- ions are also located within the red sphere. B, view of the whole barrel cavity. The 2F[o] - F[c] electron density contoured at 1 around S1, S2, and S3 is depicted in blue. It clearly indicates an elongated feature for the species located in S1 that were modeled as two disordered and partially occupied Cl^- ions. Refined occupancies are as follows: S1, 0.7/0.3; S2, 0.5; S3, 1.0. C, same view as in B after soaking the crystal in a solution containing 100 mM NaBr. The resulting anomalous Fourier map, contoured at the 4.5 level and depicted in purple, clearly shows the 3 Br^- positions in the cavity at S1, S2, and S3. Refined occupancies are as follows: S1, 0.5; S2, 0.5; S3, 1.0.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 18861-18872) copyright 2008.

Figures were selected by the author.