Abstract:
:Isoaspartyl dipeptidase (IAD) is a member of the amidohydrolase superfamily and catalyzes the hydrolytic cleavage of beta-aspartyl dipeptides. Structural studies of the wild-type enzyme have demonstrated that the active site consists of a binuclear metal center positioned at the C-terminal end of a (beta/alpha)(8)-barrel domain. Steady-state kinetic parameters for the hydrolysis of beta-aspartyl dipeptides were obtained at pH 8.1. The pH-rate profiles for the hydrolysis of beta-Asp-Leu were obtained for the Zn/Zn-, Co/Co-, Ni/Ni-, and Cd/Cd-substituted forms of IAD. Bell-shaped profiles were observed for k(cat) and k(cat)/K(m) as a function of pH for all four metal-substituted forms. The pK(a) of the group that must be unprotonated for catalytic activity varied according to the specific metal ion bound in the active site, whereas the pK(a) of the group that must be protonated for catalytic activity was relatively independent of the specific metal ion present. The identity of the group that must be unprotonated for catalytic activity was consistent with the hydroxide that bridges the two divalent cations of the binuclear metal center. The identity of the group that must be protonated for activity was consistent with the free alpha-amino group of the dipeptide substrate. Kinetic constants were obtained for the mutant enzymes at conserved residues Glu77, Tyr137, Arg169, Arg233, Asp285, and Ser289. The catalytic properties of the wild-type and mutant enzymes, coupled with the X-ray crystal structure of the D285N mutant complexed with beta-Asp-His, are consistent with a chemical reaction mechanism for the hydrolysis of dipeptides that is initiated by the polarization of the amide bond via complexation to the beta-metal ion of the binuclear metal center. Nucleophilic attack by the bridging hydroxide is facilitated by abstraction of its proton by the side chain carboxylate of Asp285. Collapse of the tetrahedral intermediate and cleavage of the carbon-nitrogen bond occur with donation of a proton from the protonated form of Asp285.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Martí-Arbona R,Fresquet V,Thoden JB,Davis ML,Holden HM,Raushel FMdoi
10.1021/bi050008rsubject
Has Abstractpub_date
2005-05-17 00:00:00pages
7115-24issue
19eissn
0006-2960issn
1520-4995journal_volume
44pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::We have used flash-detection optical and electron paramagnetic resonance spectroscopy to measure the kinetics and yield per flash of the photooxidation of cytochrome b559 and the yield per flash of the photooxidation of the tyrosine residue YD in Mn-depleted photosystem II (PSII) membranes at room temperature. The ini...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00490a014
更新日期:1990-09-25 00:00:00
abstract::To better understand how amino acid sequences specify unique tertiary folds, we have used random mutagenesis and phage display selection to evolve proteins with a high degree of sequence identity but different tertiary structures (homologous heteromorphs). The starting proteins in this evolutionary process were the Ig...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi051231r
更新日期:2005-11-01 00:00:00
abstract::Calf brain tubulin was subjected to isoelectric focusing and tryptic peptide map analysis. Results from isoelectric focusing experiments showed a total number of 17 well-resolved protein peaks. The number of peaks and the mass distribution under each peak remained the same when the concentration of protein or ampholyt...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00512a006
更新日期:1981-04-28 00:00:00
abstract::The major histocompatibility complex (HLA in humans) contains a relatively large set of gene loci in the HLA-D/DR region responsible for regulation of the immune response. The structural dissection of the protein products of these loci is a necessary accompaniment to understanding of this response. In this study, two ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00269a002
更新日期:1982-12-21 00:00:00
abstract::HIV-1 Vif is an accessory protein that induces the proteasomal degradation of the host restriction factor, apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G). The N-terminal half of Vif binds to APOBEC3G, and the C-terminal half binds to subunits of a cullin 5-based ubiquitin ligase. This Vi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi201738a
更新日期:2012-03-13 00:00:00
abstract::To identify the residues essential for interfacial binding and substrate binding of human pancreatic phospholipase A2 (hpPLA2), several ionic residues in the putative interfacial binding surface (R6E, K7E, K10E, and K116E) and substrate binding site (D53K and K56E) were mutated. Interfacial affinity of these mutants w...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi990600e
更新日期:1999-06-15 00:00:00
abstract::The functional role of distinct phospholipid subclasses and molecular species in modulating gramicidin-mediated K+ flux was characterized through quantification of changes in the fluorescence intensity of ion specific fluorescent probes encapsulated inside vesicles comprised of individual molecular species of plasmeny...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00022a008
更新日期:1995-06-06 00:00:00
abstract::The nonspecific phospholipase C from Bacillus cereus is a zinc metalloenzyme that catalyzes the hydrolysis of phospholipids to yield diacylglycerol and a phosphate monoester. Glu-4 has been proposed as a potential candidate for the general base in the hydrolysis reaction and was shown to interact with the substrate he...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi972751s
更新日期:1998-03-24 00:00:00
abstract::Helix-junction-helix (HJH) motifs are flexible building blocks of RNA architecture that help define the orientation and dynamics of helical domains. They are also frequently involved in adaptive recognition of proteins and small molecules and in the formation of tertiary contacts. Here, we use a battery of nuclear mag...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00285
更新日期:2016-08-16 00:00:00
abstract::The empoyment of a novel method of affinity chromatography, which makes use of antibodies that specifically bind DNA/RNA hybrids, has made it possible to enrich for rat rDNA molecules which contain R loops formed with the 18S and 28S rRNAs. An approximately 150-fold enrichment of the ratrRNA coding sequences was obtai...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00580a030
更新日期:1979-06-26 00:00:00
abstract::The enzyme form of the calcium adenosinetriphosphatase of sarcoplasmic reticulum (CaATPase) that is stable in the presence of calcium, cE.Ca2, has a binding site for the catalytic Mg2+ ion with a dissociation constant of 0.94 +/- 0.15 mM at 25 degrees C, pH 7.0, and 100 mM KCl. This is approximately 10 times smaller t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00077a016
更新日期:1993-07-06 00:00:00
abstract::The genomic hypervariation of human immunodeficiency virus 1 (HIV-1) could result from misincorporations by the viral reverse transcriptase. We developed an assay for reverse transcriptase fidelity during RNA-dependent as well as DNA-dependent DNA polymerization in vitro. A lacZ alpha RNA fragment transcribed by T3 RN...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00119a002
更新日期:1992-02-04 00:00:00
abstract::Beta-lactamases are the most widespread resistance mechanism to beta-lactam antibiotics, such as the penicillins and cephalosporins. Transition-state analogues that bind to the enzymes with nanomolar affinities have been introduced in an effort to reverse the resistance conferred by these enzymes. To understand the or...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi035054a
更新日期:2003-12-16 00:00:00
abstract::Although the binding of bivalent metal-ion activators to phosphoglucomutase produces substantial changes in the near ultraviolet spectrum of the enzyme, the extent to which aromatic residues are exposed to the aqueous environment, as assessed by means of solvent perturbation spectroscopy (using D2O), does not appear t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00601a031
更新日期:1978-04-18 00:00:00
abstract::The ATP-hydrolyzing portion of the proton pump from clathrin-coated vesicles (isolated from calf brain) was solubilized with three nondenaturing detergents (cholate, octyl glucoside, and Triton X-100). The hydrodynamic properties of the solubilized (Mg2+)-ATPase were then determined by sedimentation analysis in H2O an...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00363a015
更新日期:1986-07-29 00:00:00
abstract::The extrinsic 33-kDa protein (P33) was cross-linked covalently to the binding site on P33-depleted PSII preparations which is responsible for reconstitution of photosynthetic water oxidation after PSII preparations have been washed with 1 M CaCl2. Conditions were found in which more than half of the cross-linked prote...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00439a033
更新日期:1989-06-27 00:00:00
abstract::It is now accepted that two or more conformations may exist within the same DNA molecule, thereby generating conformational junctions. The presence of B-Z junctions between right- and left-handed DNA conformations has been detected in plasmids by a number of techniques. Preliminary characterization of the first exampl...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00428a046
更新日期:1989-01-24 00:00:00
abstract::Oligodeoxyribonucleotides 8-12 nucleotides in length whose sequences are complementary to the 5' end, the initiation codon regions, or the coding regions of rabbit globin mRNA were tested for their ability to inhibit translation in a rabbit reticulocyte lysate and in a wheat germ extract. The oligomers interact specif...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00343a015
更新日期:1985-10-22 00:00:00
abstract::The EcDos protein belongs to a group of heme-based sensors that detect their ligands with a heme-binding PAS domain. Among these various heme-PAS proteins, EcDos is unique in having its heme iron coordinated at both axial positions to residues of the protein. To achieve its high affinities for ligands, one of the axia...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi025845x
更新日期:2002-07-02 00:00:00
abstract::Out of over 60 single-Cys mutants in putative periplasmic loops in lactose permease, three mutants [Tyr101 --> Cys (loop III/IV), Leu313 --> Cys (loop IX/X), and Ser375 --> Cys (loop XI/XII)] spontaneously form disulfide-linked dimers, indicating that these loops are located on the periphery of the 12-helix bundle tha...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971172k
更新日期:1997-09-30 00:00:00
abstract::Elucidation of the molecular mechanism leading to biomembrane fusion is a challenging issue in current biomedical research in view of its involvement in controlling cellular functions and in mediating various important diseases. According to the generally admitted stalk mechanism described for membrane fusion, negativ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi060317x
更新日期:2006-08-01 00:00:00
abstract::The complete sequence of histone 2B of Drosophila has been determined by using an improved Beckman sequenator. Comparing these data with those previously published by other investigators on the histone 2B of calf [Iwai, K., Hayashi, H., & Ishikawa, K. (1972) J. Biochem. (Tokyo) 72, 357--367], trout [Koostra, A., & Bai...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00592a025
更新日期:1979-12-11 00:00:00
abstract::The interaction of pig plasma gelsolin (G) and actin (A) was examined by using photoreactive 4-maleimidobenzophenone-actin (BPM-actin) in which BPM was previously conjugated to Cys-374 of actin through the maleimide moiety. In the presence of micromolar [Ca2+], the major cross-linked product observed after irradiation...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00237a020
更新日期:1991-06-11 00:00:00
abstract::The insulin-linked polymorphic region (ILPR) is a regulatory sequence in the promoter region upstream of the human insulin gene and is widely recognized as a locus of type 1 diabetes susceptibility. Polymorphism of the ILPR sequence can affect expression of both insulin and the adjacent insulin-like growth factor 2 (I...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi900958x
更新日期:2009-09-01 00:00:00
abstract::A Rhodobacter sphaeroides bchD (magnesium chelatase) mutant was studied to determine the properties of its photosystem in the absence of bacteriochlorophyll (BChl). Western blots of reaction center H, M, and L (RC H/M/L) proteins from mutant membranes showed levels of 12% RC H, 32% RC L, and 46% RC M relative to those...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi701407k
更新日期:2007-10-30 00:00:00
abstract::A visual pigment consists of an opsin protein and a chromophore, 11-cis-retinal, which binds to a specific lysine residue of opsin via a Schiff base linkage. The Schiff base chromophore is protonated in pigments that absorb visible light, whereas it is unprotonated in ultraviolet-absorbing visual pigments (UV pigments...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi7003763
更新日期:2007-05-29 00:00:00
abstract::Oligomerization of numerous G protein-coupled receptors has been documented, including the prototypic family B secretin receptor. The clinical significance of oligomerization of this receptor became clear with the recent observation that a misspliced form present in pancreatic cancer could associate with the wild-type...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi060494y
更新日期:2006-07-11 00:00:00
abstract::The anomeric proton (H-1) chemical shifts of D-mannopyranosides in aqueous solution are affected both by the aglycon and by substitution of the ring [Lee, Y. C., & Ballou, C. E. (1965) Biochemistry 4, 257]. We have examined the 1H NMR spectra for a variety of linear and branched mannooligosaccharides and have assigned...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00559a031
更新日期:1980-09-02 00:00:00
abstract::Magic angle sample spinning (MASS) 13C NMR spectra have been obtained of bovine rhodopsin regenerated with retinal prosthetic groups isotopically enriched with 13C at C-5 and C-14. In order to observe the 13C retinal chromophore resonances, it was necessary to employ low temperatures (-15-----35 degrees C) to restrict...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00380a018
更新日期:1987-03-24 00:00:00
abstract::As part of a search for peptides that have specificity for selected protein kinases, the possibility that adenosine cyclic 3',5'-phosphate dependent protein kinase (A-kinase) recognizes the hydrogen-bonding potential of its peptide substrates was investigated. A-Kinase catalyzes the phosphorylation of five N alpha-met...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00388a041
更新日期:1987-07-14 00:00:00