Molecular structure of biotin. Results of two independent crystal structure investigations

Abstract

The three-dimensional crystal structure of d-(+)-biotin, the coenzyme responsible for the fixation and transfer of carbon dioxide in biological systems, has been determined by x-ray diffraction techniques in two laboratories independently. The results of the two determinations are compared and discussed in terms of the mode of nucleophilic activation of the coenzyme. Of particular relevance may be the participation of the ureido carbonyl oxygen as acceptor of a strong hydrogen bond ( 0 . . . O distance 2.54 A) which may cause the observed lengthening of the ureido carbonyl bond to 1.25 8, and shortening of the carbonyl carbon-nitrogen bonds to 1.33 and 1.35 A. These results suggest a partial delocalization of the electronic charge within the ureido group, and are supportive of a proposed activation via polarization mechanism. A close intramolecular nonbonded contact involving the nitrogen atom proximal to the valeryl chain probably precludes carboxylation from that side of the molecule.Biotin (I) participates as coenzyme in a variety of carboxylase, decarboxylase, and transcarboxylase systems. Its role is to fix CO2 for eventual transfer, and it accomplishes its task in a two-step fashion during which a labile enzymebiotin-COz complex is formed.2 Early crystallographic 02'II studies of biotin by Traub3 confirmed the relative stereochemistry a t the asymmetric carbons previously suggested by Grob and von S p r e~h e r .~ In studies of the biotin carboxylation mechanism Bonnemere, Hamilton, Steinrauf, and Knappej prepared the bis-p-bromoanilide derivative of the major product in the biotin methyl ester-methyl chloroformate reaction and, by crystallographic determination, confirmed that the primary site of carboxylation in this model reaction was the ureido 1'-N nitrogen. Knappe had already shown that the major product had identical properties with the dimethyl ester of carboxybiotin obtained by diazomethane trapping experiments in biological systems. Subsequently Trotter and Hamilton6 measured the anomalous dispersion properties of the same compound, 1 '-N-carboxybiotin bis-p-bromoanilide, and established the absolute configuration of biotin.Continued interest in the mode of action of biotin-dependent enzymes as well as our own interest in careful structural investigation of the biotin vitamers prompted a reinvestigation of the biotin crystal structure, and ultimately led to its determination by two groups working independently of the other. A collaborative report of our results is presented. Where necessary to distinguish between the results of the two groups, work performed by DeTitta and Edmonds, Medical Foundation of Buffalo, is designated I, and by Stallings and Donohue, University of Pennsylvania, 11. Experimental SectionI. Needle-shaped crystals elongated about the a axis were grown by slow cooling of an aqueous solution of biotin (Sigma Co. Lot no. 12C-2000) saturated at 95 'C. A crystal of cross section 0.05 X 0.14 mm and length 0.88 mm was cleaved from a longer crystal and mounted about the a axis for da...

Relationship between molecular structure and supramolecular morphology of DODA-EO2-biotin and related lipids

“…These properties might be of importance in providing a favorable orientation of the biotin molecules for stacking interactions. Several additional elements support the idea that biotin groups have a tendency to form stacked assemblies: (i) their molecular packing observed in the crystal structure reveals a stacking of the biotin rings along one of the crystal axes (DeTitta et al, 1976); and (ii) the concentration of biotin molecules used in our experiments is close to the limit of solubility of biotin in aqueous solutions (0.9 mM). Although interactions between biotin moieties are likely to stabilize the lipid tubules, some of the biotin groups must have a minimal degree of freedom necessary for binding streptavidin molecules.…”

“…The absence of tubes with lipids 3 and 5-8 enables to draw some conclusions on the structural elements required to induce the tubular morphology. The fact that both DODA-EO 2 -NH 2 and DODA-EO 2 -desthiobiotin molecules lack the molecular characteristics responsible for the tube formation further indicates that the presence and integrity of the biotin moiety, which presents three asymmetric carbon atoms in a cis-cis configuration (Traub, 1958;DeTitta et al, 1976), constitutes a crucial requirement. DODA-EO 2 -desthiobiotin differs from DODA-EO 2 -biotin by the lack of the thio moiety in the biotin group, resulting in a more flexible head group lacking the asymmetric carbon position defining the D-enantiomery of the biotin.…”

Tetrahydro-6-methyl-1H,3H-thieno[3,4-b]pyrrol-2-one, an Analogue of Biotin

“…1. The bicyclic tetrahydrothienopyrrolidone system has a conformation similar to that reported for the tetrahydrothienoimidazolone system in biotin (DeTitta, Edmonds, Stallings & Donohue, 1976). The bicyclic moiety has pseudo-mirror symmetry about a plane containing atoms C2 and $5, and normal to the C3a--C6a bond, with an asymmetry parameter (Duax & Norton, 1975) C~ of 0.7 ° (cf.…”

A mechanism for the transfer of the carboxyl‐group from 1'‐N‐carboxybiotin to acceptor substrates by biotin‐containing enzymes

“…N-carboxyimidazolidone, a model compound for carboxybiotin, loses its carboxyl group by an intramolecular cyclic decarboxylation reaction and has no tendency to transfer it to a nucleop~le 1121. Crystal structure analyses of biotin [17] and N-methoxycarbonyl biotin methyl ester [16] indicate that the carboxylation of biotin decreases its ability to withdraw a proton from a substrate. Furthermore, of the 3 compounds that participate in the tr~sc~boxyl~e reaction (oxaloacetate, carboxybiotin and methylm~onyl-CoA), c~boxybiotin is the most stable [lg].…”