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Coenzyme Binding (coenzyme + binding)
Selected AbstractsCrystal structure of archaeal highly thermostable L -aspartate dehydrogenase/NAD/citrate ternary complexFEBS JOURNAL, Issue 16 2007Kazunari Yoneda The crystal structure of the highly thermostable l -aspartate dehydrogenase (l -aspDH; EC 1.4.1.21) from the hyperthermophilic archaeon Archaeoglobus fulgidus was determined in the presence of NAD and a substrate analog, citrate. The dimeric structure of A. fulgidusl -aspDH was refined at a resolution of 1.9 Ĺ with a crystallographic R -factor of 21.7% (Rfree = 22.6%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. Structural comparison of the A. fulgidusl -aspDH/NAD/citrate ternary complex and the Thermotoga maritimal -aspDH/NAD binary complex showed that A. fulgidusl -aspDH assumes a closed conformation and that a large movement of the two loops takes place during substrate binding. Like T. maritimal -aspDH, the A. fulgidus enzyme is highly thermostable. But whereas a large number of inter- and intrasubunit ion pairs are responsible for the stability of A. fulgidusl -aspDH, a large number of inter- and intrasubunit aromatic pairs stabilize the T. maritima enzyme. Thus stabilization of these two l -aspDHs appears to be achieved in different ways. This is the first detailed description of substrate and coenzyme binding to l -aspDH and of the molecular basis of the high thermostability of a hyperthermophilic l -aspDH. [source] Prediction of coenzyme specificity in dehydrogenases/ reductasesFEBS JOURNAL, Issue 6 2006A hidden Markov model-based method, its application on complete genomes Dehydrogenases and reductases are enzymes of fundamental metabolic importance that often adopt a specific structure known as the Rossmann fold. This fold, consisting of a six-stranded ,-sheet surrounded by ,-helices, is responsible for coenzyme binding. We have developed a method to identify Rossmann folds and predict their coenzyme specificity (NAD, NADP or FAD) using only the amino acid sequence as input. The method is based upon hidden Markov models and sequence pattern analysis. The prediction sensitivity is 79% and the selectivity close to 100%. The method was applied on a set of 68 genomes, representing the three kingdoms archaea, bacteria and eukaryota. In prokaryotes, 3% of the genes were found to code for Rossmann-fold proteins, while the corresponding ratio in eukaryotes is only around 1%. In all genomes, NAD is the most preferred cofactor (41,49%), followed by NADP with 30,38%, while FAD is the least preferred cofactor (21%). However, the NAD preponderance over NADP is most pronounced in archaea, and least in eukaryotes. In all three kingdoms, only 3,8% of the Rossmann proteins are predicted to have more than one membrane-spanning segment, which is much lower than the frequency of membrane proteins in general. Analysis of the major protein types in eukaryotes reveals that the most common type (26%) of the Rossmann proteins are short-chain dehydrogenases/reductases. In addition, the identified Rossmann proteins were analyzed with respect to further protein types, enzyme classes and redundancy. The described method is available at http://www.ifm.liu.se/bioinfo, where the preferred coenzyme and its binding region are predicted given an amino acid sequence as input. [source] Interflavin electron transfer in human cytochrome P450 reductase is enhanced by coenzyme bindingFEBS JOURNAL, Issue 12 2003Relaxation kinetic studies with coenzyme analogues The role of coenzyme binding in regulating interflavin electron transfer in human cytochrome P450 reductase (CPR) has been studied using temperature-jump spectroscopy. Previous studies [Gutierrez, A., Paine, M., Wolf, C.R., Scrutton, N.S., & Roberts, G.C.K. Biochemistry (2002) 41, 4626,4637] have shown that the observed rate, 1/,, of interflavin electron transfer (FADsq , FMNsq,FADox , FMNhq) in CPR reduced at the two-electron level with NADPH is 55 ± 2 s,1, whereas with dithionite-reduced enzyme the observed rate is 11 ± 0.5 s,1, suggesting that NADPH (or NADP+) binding has an important role in controlling the rate of internal electron transfer. In relaxation experiments performed with CPR reduced at the two-electron level with NADH, the observed rate of internal electron transfer (1/, = 18 ± 0.7 s,1) is intermediate in value between those seen with dithionite-reduced and NADPH-reduced enzyme, indicating that the presence of the 2,-phosphate is important for enhancing internal electron transfer. To investigate this further, temperature jump experiments were performed with dithionite-reduced enzyme in the presence of 2,,5,-ADP and 2,-AMP. These two ligands increase the observed rate of interflavin electron transfer in two-electron reduced CPR from 1/, = 11 s,1 to 35 ± 0.2 s,1 and 32 ± 0.6 s,1, respectively. Reduction of CPR at the two-electron level by NADPH, NADH or dithionite generates the same spectral species, consistent with an electron distribution that is equivalent regardless of reductant at the initiation of the temperature jump. Spectroelectrochemical experiments establish that the redox potentials of the flavins of CPR are unchanged on binding 2,,5,-ADP, supporting the view that enhanced rates of interdomain electron transfer have their origin in a conformational change produced by binding NADPH or its fragments. Addition of 2,,5,-ADP either to the isolated FAD-domain or to full-length CPR (in their oxidized and reduced forms) leads to perturbation of the optical spectra of both the flavins, consistent with a conformational change that alters the environment of these redox cofactors. The binding of 2,,5,-ADP eliminates the unusual dependence of the observed flavin reduction rate on NADPH concentration (i.e. enhanced at low coenzyme concentration) observed in stopped-flow studies. The data are discussed in the context of previous kinetic studies and of the crystallographic structure of rat CPR. [source] Enhancement of coenzyme binding by a single point mutation at the coenzyme binding domain of E. coli lactaldehyde dehydrogenasePROTEIN SCIENCE, Issue 3 2008José Salud Rodríguez-Zavala Abstract Phenylacetaldehyde dehydrogenase (PAD) and lactaldehyde dehydrogenase (ALD) share some structural and kinetic properties. One difference is that PAD can use NAD+ and NADP+, whereas ALD only uses NAD+. An acidic residue has been involved in the exclusion of NADP+ from the active site in pyridine nucleotide-dependent dehydrogenases. However, other factors may participate in NADP+ exclusion. In the present work, analysis of the sequence of the region involved in coenzyme binding showed that residue F180 of ALD might participate in coenzyme specificity. Interestingly, F180T mutation rendered an enzyme (ALD-F180T) with the ability to use NADP+. This enzyme showed an activity of 0.87 ,mol/(min * mg) and Km for NADP+ of 78 ,M. Furthermore, ALD-F180T exhibited a 16-fold increase in the Vm/Km ratio with NAD+ as the coenzyme, from 12.8 to 211. This increase in catalytic efficiency was due to a diminution in Km for NAD+ from 47 to 7 ,M and a higher Vm from 0.51 to 1.48 ,mol/(min * mg). In addition, an increased Kd for NADH from 175 (wild-type) to 460 ,M (mutant) indicates a faster product release and possibly a change in the rate-limiting step. For wild-type ALD it is described that the rate-limiting step is shared between deacylation and coenzyme dissociation. In contrast, in the present report the rate-limiting step in ALD-F180T was determined to be exclusively deacylation. In conclusion, residue F180 participates in the exclusion of NADP+ from the coenzyme binding site and disturbs the binding of NAD+. [source] | ||||||||||