SFLD - Family - Glycerol dehydratase activase

Top Level Name

⌊ Superfamily (core) Radical SAM

⌊ Subgroup organic radical-activating enzymes


	Total	100%	<100%
Functional domains	5	5	0
UniProtKB	22	22	0
GI	42	42	0
Structures	0
Reactions	1
Functional domains of this family were last updated on June 10, 2017
New functional domains were last added to this family on June 22, 2014

Glycerol dehydratase activase (GD-AE) contains the canonical [Fe4S4] binding motif and two additional ferredoxin-like [4Fe-4S] cluster binding domains. It is an organic radical activase that forms a glycyl radical on the B12-independent glycerol dehydratase and, counter to the paradigm of the common activation step of the Radical SAM superfamily, produces 5′-deoxy-5′-(methylthio)adenosine (MTA) and 2-aminobutyrate rather than 5′-deoxyadenosine (5'-dA) and methionine. The formation of MTA rather than 5'-dA is somewhat analagous to the Radical SAM 3-amino-3-carboxypropyl radical forming Superfamily and thus a similar radical intermediate has been proposed. This alternative reductive cleavage pathway for SAM is surprising given the structural similarities between the GD and PFL at the level of both primary and tertiary structure, it is difficult at this time to determine exactly why the GD-AE follows a different reductive cleavage pathway during glycyl radical formation. The precise identity of the radical intermediate in the GD-AE activation mechanism is still under investigation.

Demick JM, Lanzilotta WN

Radical SAM activation of the B12-independent glycerol dehydratase results in formation of 5'-deoxy-5'-(methylthio)adenosine and not 5'-deoxyadenosine

▸ Abstract

Biochemistry 2011;50(4):440-442 | PubMed ID: 21182298

Raynaud C, Sarçabal P, Meynial-Salles I, Croux C, Soucaille P

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum

▸ Abstract

Proc Natl Acad Sci U S A 2003;100(9):5010-5015 | PubMed ID: 12704244

O'Brien JR, Raynaud C, Croux C, Girbal L, Soucaille P, Lanzilotta WN

Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization

▸ Abstract

The molecular characterization of a B12-independent glycerol dehydratase from Clostridium butyricum has recently been reported [Raynaud, C., et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 5010-5015]. In this work, we have further characterized this system by biochemical and crystallographic methods. Both the glycerol dehydratase (GD) and the GD-activating enzyme (GD-AE) could be purified to homogeneity under aerobic conditions. In this form, both the GD and GD-AE were inactive. A reconstitution procedure, similar to what has been reported for pyruvate formate lyase activating enzyme (PFL-AE), was employed to reconstitute the activity of the GD-AE. Subsequently, the reconstituted GD-AE could be used to reactivate the GD under strictly anaerobic conditions. We also report here the crystal structure of the inactive GD in the native (2.5 A resolution, Rcryst = 17%, Rfree = 20%), glycerol-bound (1.8 A resolution, Rcryst = 21%, Rfree = 24%), and 1,2-propanediol-bound (2.4 A resolution, Rcryst = 20%, Rfree = 24%) forms. The overall fold of the GD monomer was similar to what has been observed for pyruvate formate lyase (PFL) and anaerobic ribonucleotide reductase (ARNR), consisting of a 10-stranded beta/alpha barrel motif. Clear density was observed for both substrates, and a mechanism for the dehydration reaction is presented. This mechanism clearly supports a concerted pathway for migration of the OH group through a cyclic transition state that is stabilized by partial protonation of the migrating OH group. Finally, despite poor alignment (rmsd approximately 6.8 A) of the 10 core strands that comprise the barrel structure of the GD and PFL, the C-terminal domains of both proteins align well (rmsd approximately 0.7 A) and have structural properties consistent with this being the docking site for the activating enzyme. A single point mutation within this domain, at a strictly conserved arginine residue (R782K) in the GD, resulted in formation of a tight protein-protein complex between the GD and the GD-AE in vivo, thereby supporting this hypothesis.

Biochemistry 2007;43(16):4634-4645 | PubMed ID: 15096031

Gene: dhaB2

Static File Downloads

File Name	Description	Parameters	Stats
network.fam298.bs60.mek250K.xgmml	One node per sequence network	min bit score = 60 max edge count = 250K	size = 17K num_edges = 10 num_nodes = 5
sfld_alignment_fam298.msa	Annotated Sequence Alignment, Stockholm format		3 sequences size: 2.1K

Catalyzed Reaction(s)

[glycerol dehydratase]-activating enzyme

glycerol dehydratase (inactive)
1r8w

S-adenosyl-L-methioninate
67040

1,5-dihydroflavin
62787

glycerol dehydratase (active)
1r8w

L-methionine zwitterion
57844

5'-deoxyadenosine
17319

semiquinone
15817