Crystal structure of a photolysis product of vitamin B 6 : A pyridodihydrofuran-condensed skeleton compound of pyridoxal 5′-phosphate

2017 ◽  
Vol 1148 ◽  
pp. 57-61
Author(s):  
Katsuyuki Aoki ◽  
Hideyuki Nakamura ◽  
Toshiaki Hattori ◽  
Ning-Hai Hu ◽  
Masayoshi Onishi
2014 ◽  
Vol 70 (4) ◽  
pp. 1166-1172 ◽  
Author(s):  
Michael E. Webb ◽  
Briony A. Yorke ◽  
Tom Kershaw ◽  
Sarah Lovelock ◽  
Carina M. C. Lobley ◽  
...  

Aspartate α-decarboxylase is a pyruvoyl-dependent decarboxylase required for the production of β-alanine in the bacterial pantothenate (vitamin B5) biosynthesis pathway. The pyruvoyl group is formedviathe intramolecular rearrangement of a serine residue to generate a backbone ester intermediate which is cleaved to generate an N-terminal pyruvoyl group. Site-directed mutagenesis of residues adjacent to the active site, including Tyr22, Thr57 and Tyr58, reveals that only mutation of Thr57 leads to changes in the degree of post-translational activation. The crystal structure of the site-directed mutant T57V is consistent with a non-rearranged backbone, supporting the hypothesis that Thr57 is required for the formation of the ester intermediate in activation.


2014 ◽  
Vol 70 (12) ◽  
pp. 1584-1590 ◽  
Author(s):  
Michael C. Thompson ◽  
Christopher S. Crowley ◽  
Jeffrey Kopstein ◽  
Thomas A. Bobik ◽  
Todd O. Yeates

The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 Å resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented and the potential relevance of the observed protein–ligand interaction is briefly discussed. This work represents the first structure of a bacterial microcompartment shell protein bound to a potentially relevant cofactor molecule.


A hexacarboxylic acid, obtained by the degradation of vitamin B 12 by Cannon, Johnson & Todd in 1953 has been examined by X-ray analytical methods. These lead to a solution of both the crystal and chemical structure of the acid. The crystals are orthorhombic, a = 24·58, b = 15·52, c = 13·32 Å, space group, P 2 1 2 1 2 1 , n = 4. The asymmetric unit is found to consist essentially of one molecule of hexacarboxylic acid, C 46 H 58 O 13 N 6 . CoCl, two molecules of water and one of acetone. The hexacarboxylic acid molecule has a central cobalt atom in approximately octahedral co-ordination attached to one cyanide group, one chlorine atom and four nitrogen atoms of the corrin nucleus. The nucleus itself is substituted by acetic and propionic acid groups, a lactam ring and a number of methyl groups. The position of the cobalt atom in the crystal structure was first found from Patterson projections and the remaining atomic positions then derived from a series of calculated approximations to the three-dimensional electron density distribution. For these calculations, phases were derived from structure factors calculated on gradually increasing numbers of selected atomic positions from the stage of ρ 1, where only the cobalt atom sites were known, to ρ 10 where 73 atoms, not counting hydrogen, had been placed. The process was not quite straightforward; particular difficulty was experienced in finding the positions of the atoms of one side-chain which may be affected by disorder. The parameters of the atoms have been refined by two cycles of least-squares calculations. A number of observations were made in the course of the analysis which bear on the further use of non-centrosymmetric Fourier syntheses in the study of complex structures. An appendix by A. Vos deals with intensity anomalies observed on the X-ray photographs of the hexacarboxylic acid which provide evidence of its absolute configuration. An appendix by K. N. Trueblood summarizes various aspects of the analysis of the hexacarboxylic acid, seen as a whole.


The crystal structure of vitamin B 12 -5' -phosphate, a biosynthetic precursor of vitamin B 12 , has been determined by X-ray diffraction methods. The air-dried crystals are orthorhombic, space group P 2 1 2 1 2 1 , with a = 23.72 Å, b = 21.74 Å and c = 16.07 Å. The observed density of 1.362 g cm -3 indicates four vitamin B 12 -5' -phosphate and about sixty water molecules in the unit cell. The X-ray diffraction data to 1.2 Å resolution were collected with a PAILRED linear diffractometer using Cu K α radiation from a silicon monochromator. The structure was solved by using Patterson methods in conjunction with the tangent formula and was refined by Fourier and least-squares methods. The final R value for the 2112 observed reflexions is 16.2 %. The structure is very similar to that found by Hodgkin and co-workers for air-dried vitamin B 12 crystals. The difference Fourier synthesis between this compound and vitamin B 12 shows that two water molecules move into phosphate oxygen positions when the phosphate in the precursor is removed, and one acetamide in contact with these water molecules in the vitamin is rotated out of the way in the phosphate. A second acetamide is also differently oriented in the two crystals. The α -glycosidic bond between the ribose and the dimethylbenzimidazole is 16° out of the plane of the base. The ribose conformation is C2'>- exo , and the phosphate ester conformations are similar to those found in other B 12 crystals.


Measurements were made during 1948-9 of all the intensities of hkl reflexions observable with chromium Koc X-radiation from air-dried crystals of vitamin B 12 . Calculations parallel with those of J. G. White were carried out on these data. The positions of the cobalt atoms in the crystal structure were found from three-dimensional Patterson series and the positions of 90 atoms of the B 12 molecule and 7 water molecules were derived through three successive approximations to the three-dimensional electron density distribution. The choice of atomic positions was checked against superposition maps derived from the original Patterson series, and assisted by comparisons with other B 12 derivatives. Minor differences appear between the positions derived here and in III; some of these may be real differences due to the state of dryness of the crystals.


1998 ◽  
Vol 54 (1) ◽  
pp. 94-96 ◽  
Author(s):  
E. B. Starikov ◽  
T. Steiner

The neutron diffraction crystal structure of vitamin B12 coenzyme [Bouquiere et al. (1993). Acta Cryst. B49, 79–89] contains a yet unnoticed intramolecular aromatic hydrogen bond donated by a propionamide side chain and accepted by the benzimidazole group. The distance from the H-atom to the aromatic midpoint is only 2.58 Å and the bond energy is calculated to be 16.7 kJ mol−1.


2003 ◽  
Vol 185 (14) ◽  
pp. 4163-4171 ◽  
Author(s):  
Florian Schmitzberger ◽  
Alison G. Smith ◽  
Chris Abell ◽  
Tom L. Blundell

ABSTRACT Escherichia coli ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first step in the biosynthesis pathway of pantothenate (vitamin B5), the transfer of a hydroxymethyl group onto α-ketoisovalerate. Here we describe a detailed comparative analysis of the KPHMT crystal structure and the identification of structural homologues, some of which have remarkable similarities in their active sites, modes of binding to substrates, and mechanisms. We show that KPHMT forms a family within the phosphoenolpyruvate/pyruvate superfamily. Based on the analysis, we propose that in this superfamily there should be a subdivision into two groups. This paper completes our structural analysis of the E. coli enzymes in the pantothenate pathway.


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