Cobalamines, conformation

Figure 15.8 (a) Structure and (b) alternative conformations of cobalamine found in B12-dependent enzymes. The functional group R is deoxyadenosine in AdoCbl, methyl in MeCbl and -CN in vitamin B12. (From Bannerjee and Ragsdale, 2003. Reprinted with permission from Annual Reviews.)... 

Cinnamic acid, 268 Cobalamin, 236 Colititol, 285 Colitose, 284, 311 Colominic acid, 233, 296, 336,337 Conformational analysis, 11,12 Conformations, during anomerization, 42... 

The half-wave potential for the enzyme-bound Co VCo cobalamin couple of the methionine synthase from E. coli at 526 mV versus SHE is about 80 mV lower than that of the Co /Cokcobalamin couple in neutral aqueous solution. Access to the catalytic cycle of the enzyme by one-electron reduction of Co kcobalamin (and reactivation upon occasional adventitious formation of Co -cobalamin) is indicated to be accomplished by a unique mechanism. The (thermodynamically unfavorable) reduction with intermediate formation of the enzyme-bound Cokcobalamin is driven by a rapid methylation of the highly reduced Co -center of the reduced corrin with Y-adenosyhnethionine. The modular nature of methionine synthase allows for the control of the methyl-group transfer processes by modulating and alternating conformational equilibria. ... 

The vitamin B12 and related coenzymes (cobalamins, cobinamides, and corrinoids) have been studied in detail using H and shift and relaxation studies. (595-598) With the aid of lanthanide probes the eonformations of cobalamins in solution are shown to be very similar to those in the crystalline state. The appreciable temperature dependences of the electronic and H NMR spectra are attributed to a conformational change rather than to a 6-eoordinate-5-coordinate equilibrium as previously suggested. (599) The binding of 5 -ATP to the respiratory protein hemoeyanin has been studied by H and NMR. 

Bandarian V, Ludwig ML, Matthews RG. (2002) Factors modulating conformational equilibria in large modular proteins a case study with cobalamin-dependent methionine synthase. Proc Natl Acad Sci USA 100 8156-8163. 

Studies on protein-free corrinoids and model complexes have shown that increasing the steric bulkiness around the coordinated Ca atom can cause a dramatic labilization of the Co—C bond. The protein-coenzyme adduct might contain the coenzyme in a resting state and the protein in a strained state the substrate would then switch the system into a strained coenzyme and a relaxed enzyme with little thermodynamic barrier. The strained form of the coenzyme is then in labile equilibrium with base-on cobalt(II) and the free radical. " This hypothesis, that conformational changes in cobalamin can switch chemical reactions on and off, is closely analogous with the known aspects of hemoglobin function. 

The structure in Figure 28 contains information potentially pertaining to translocation of the methylene group of the 5-deoxyadenosyl radical from Co of cobalamin to the substrate 6 A away. The structure shows two conformations of the ribosyl ring in 5-deoxyadenosine, the C2 -endo and the CV-endo conformations. The two conformations project the 5 -methyl group 3.1 and 4.5 A, respectively, from Co. The orientation in the Cy-endo conformation, if replicated in the 5-deoxyadenosyl radical, would allow the methylene radical to... 

The Cobalamin-Binding Fragment [650-896] and the Nucleotide-Off Conformation of Cobalamin... 

The shape of the activation domain and the location of bound AdoMet (4), shown in Figure 3, prompted us to model a conformation competent for the reaction of AdoMet with cob(I) MetH, in which the activation domain would displace the helical cap that covers the methyl face of the corrin in the isolated cobalamin-binding fragment (5). Determination of the structure of the [649-... 

Figure 5. The structure of the activation complex (left) with the activation domain enclosing the cobalamin and part of the Bj binding domain, and the cap domain at the lower right. The cobalamin cofactor, with its side chain protruding into the B 12-binding domain, is shown in ball-and-stick mode. AdoMet has been included at the site where it binds in the isolated activation domain 4). From cross-linking experiments 49), it is known that flavodoxin binds to this face of the gactivation complex. On the right is a model for the structure of the [649-1227] fragment in its cap-on conformation. The motions of the activation and cap domains that occur in the interconversion of conformations involve rotations around axes that are not parallel to one another.

Figure 6. A stereoview showing how bound cobalamin is displaced in the activation complex. The protein structures were aligned by matching atoms from the B]2-binding domains (displayed as ribbons). The cofactor from the activation conformation is represented by the thicker bonds, and the peptide sequence Ala-Met-Trp-Pro-Gly-Ala from the activation domain is drawn in ball-and-stick mode at the left. Overlaps between the corrin in its cap-on conformation (thin bonds) and atoms of Ala 1170 and Gly 1174 are avoided by the upward movement of the corrin macrocycle.

In contrast, the activation conformation appears to be unpopulated in methylated MetH. The methylcob(III)alamin enzyme retains the spectral signature of base-on cobalamin in the presence of flavodoxin and flavodoxin is not bound (K is > 70 pM) 4 ). These observations imply that AG for dissociation of histidine from cobalt is much more positive in methylcobalamin MetH than in the cob(II)alamin form of the enzyme. 

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