Abstract:
:Urease from Klebsiella aerogenes [Jabri et al. (1995) Science 268, 998-1004] is an (alpha beta gamma)3 trimer with each alpha-subunit having an (alpha beta)8-barrel domain containing a binickel active center. Here we examine structure-function relations for urease in more detail through structural analysis of the urease apoenzyme at 2.3 A resolution and mutants of two key catalytic residues (H219A and H320A) at 2.5 A resolution. With the exception of the active site, in which a water molecule takes the place of the missing carbamate and nickel atoms, the structure of the apoenzyme is nearly identical to that of the holoenzyme, suggesting a high degree of preorganization which helps explain the tight binding of nickel. In the structure of H219A, the major change involves a conformational shift and ordering of the active site flap, but a small shift in the side chain of Asp alpha 221 could contribute to the lower activity of H219A. In the H320A structure, the catalytic water, primarily a Ni-2 ligand in the holoenzyme, shifts into a bridging position. This shift shows that the nickel ligation is rather sensitive to the environment and the change in ligation may contribute to the 10(5)-fold lower activity of H320A. In addition, these results show that urease is resilient to the loss of nickel ions and mutations. Analysis of the urease tertiary/quaternary structure suggests that the stability of this enzyme may be largely due to its burial of an unusually large fraction of its residues: 50% in the gamma-subunit, 30% in the beta-subunit, and 60% in the alpha-subunit.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Jabri E,Karplus PAdoi
10.1021/bi960424zsubject
Has Abstractpub_date
1996-08-20 00:00:00pages
10616-26issue
33eissn
0006-2960issn
1520-4995pii
bi960424zjournal_volume
35pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Stopped-flow and laser photolysis methods have been used to investigate the rates of electron-transfer reactions of fully reduced riboflavin and the three oxidation states of Clostridium pasteurianum flavodoxin. Both normal and 7,8-dichloroflavin analogues were studied. Redox reagents included oxygen, ferricyanide, fe...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00521a005
更新日期:1981-09-01 00:00:00
abstract::A study of the regular secondary structure elements of recombinant human interleukin-1 beta has been carried out using NMR spectroscopy. Using a randomly 15N labeled sample, a number of heteronuclear three- and two-dimensional NMR experiments have been performed, which have enabled a complete analysis of short-, mediu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00471a023
更新日期:1990-05-15 00:00:00
abstract::Amyloid fibrils have been classically defined as linear, nonbranched polymeric proteins with a cross beta-sheet structure and the ability to alter the optical properties of the amyloid-specific dye Congo Red. Mounting evidence suggests that soluble oligomeric peptide assemblies approximately 2-20 nm in diameter are cr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700247y
更新日期:2007-06-19 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::The plasma membrane of the cell is a complex, tightly regulated, heterogeneous environment shaped by proteins, lipids, and small molecules. Ca2+ ions are important cellular messengers, spatially separated from anionic lipids. After cell injury, disease, or apoptotic events, anionic lipids are externalized to the outer...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b01069
更新日期:2018-12-18 00:00:00
abstract::To identify interactions between Ste2p, a G protein-coupled receptor of the yeast Saccharomyces cerevisiae, and its tridecapeptide ligand, alpha-factor (WHWLQLKPGQPMY), a variety of alpha-factor analogues were used in conjunction with site-directed mutagenesis of a targeted portion of Ste2p transmembrane domain six. A...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi026100u
更新日期:2002-11-19 00:00:00
abstract::Detailed information on room-temperature structure and oxidation state of the Photosystem II (PS II) manganese complex is needed to put mechanistic considerations on solid grounds. Because previously this information had not been available, the tetranuclear manganese complex was investigated by X-ray absorption spectr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9924258
更新日期:2000-06-20 00:00:00
abstract::Administration of pregnenolone-16 alpha-carbonitrile (PCN) to adult female rats caused a 2-fold increase in total liver microsomal cytochrome P-450 along with 5-7-fold increases in four in vitro monooxygenase activities considered diagnostic for the major PCN-inducible cytochrome P-450 isozyme. However, upon administr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00387a022
更新日期:1987-06-30 00:00:00
abstract::In the course of measuring the concentrations of retinoic acids (RA) in bovine plasma, a major peak was observed which comigrated with 9-cis-RA on normal-phase high-performance liquid chromatography. Rechromatography of this retinoic on reverse-phase high-performance liquid chromatography showed that it was distinct f...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00004a013
更新日期:1995-01-31 00:00:00
abstract::The function of Lys-59, Arg-141, and Arg-277 in PAPS binding and catalysis of the flavonol 3-sulfotransferase was investigated. Affinity chromatography of conservative mutants with PAPS analogues allowed us to determine that Lys-59 interacts with the 5' portion of the nucleotide, while Arg-141 interacts with the 3' po...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi982239m
更新日期:1999-03-30 00:00:00
abstract::DrrA and DrrB proteins form an ATP-dependent efflux pump for doxorubicin and daunorubicin in Streptomyces peucetius. DrrA, the catalytic subunit, forms a complex with the integral membrane protein DrrB. Previous studies have provided evidence for strong interaction between these two proteins, which was found to be cri...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi701699a
更新日期:2008-03-04 00:00:00
abstract::With respect to the functional importance attributed to the N-terminal part of the Na(+)/proline transporter of Escherichia coli (PutP), we report here on the structural arrangement and functional dynamics of transmembrane domains (TMs) II and III and the adjoining loop regions. Information on membrane topography was ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992442x
更新日期:2000-04-25 00:00:00
abstract::To gain insight into the mechanism by which Arg-163 influences oligomerization of alphaA-crystallin, we prepared a series of truncated alphaA-crystallins with or without mutation of the Arg-163 residue. Expression of the proteins was achieved in Escherichia coli BL21 (DE3) pLysS cells, and alphaA-crystallin was purifi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi060705z
更新日期:2006-12-26 00:00:00
abstract::Phospholipase A(2) (PLA(2)) (E. C. 3.1.1.4) is a common enzyme in the two-way cascade mechanism leading to the production of proinflammatory compounds known as eicosanoids. The binding of phospholipase A(2) to the membrane surface and hydrolysis of phospholipids are thought to involve the formation of a hydrophobic ch...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi035076x
更新日期:2003-10-14 00:00:00
abstract::Several 3-oxo-4-aza steroids (1) have been identified as inhibitors of the 3 beta-hydroxy-delta 5-steroid dehydrogenase/3-keto-delta 5-steroid isomerase catalyzed conversion of pregnenolone to progesterone. By kinetically decoupling the two enzyme activities isolated from bovine adrenal cortex, it has been demonstrate...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00427a021
更新日期:1989-01-10 00:00:00
abstract::A cDNA designated hIIB1, representing the entire coding sequence of a P450 in the IIB gene family, was isolated from a human liver lambda gt11 library by using the rat IIB1 cDNA as a probe. The hIIB1 protein, deduced from the cDNA sequence, contained 491 amino acids, had a calculated molecular weight of 56,286, and di...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00444a029
更新日期:1989-09-05 00:00:00
abstract::The L-type Ca(2+) channel Ca(v)1.2 forms macromolecular signaling complexes that comprise the β(2) adrenergic receptor, trimeric G(s) protein, adenylyl cyclase, and cAMP-dependent protein kinase (PKA) for efficient signaling in heart and brain. The protein phosphatases PP2A and PP2B are part of this complex. PP2A coun...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi101018c
更新日期:2010-12-07 00:00:00
abstract::Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein (RNP) granules primarily composed of translationally repressed mRNAs and proteins related to mRNA decay, suggesting roles in post-transcriptional regulation. P-bodies are conserved in eukaryotic cells and exhibit properties of liquid droplets. However, the...
journal_title:Biochemistry
pub_type: 杂志文章,评审
doi:10.1021/acs.biochem.7b01162
更新日期:2018-05-01 00:00:00
abstract::The exchangeability of apolipoprotein (apo) E between lipoprotein particles such as very low-density lipoprotein (VLDL) and high-density lipoprotein (HDL) is critical for lipoprotein metabolism, but despite its importance, the kinetics and mechanism of apoE-lipoprotein interaction are not known. We have used surface p...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9000694
更新日期:2009-04-07 00:00:00
abstract::The fluorophore 4-heptadecyl-7-hydroxycoumarin was used as a probe to study the properties of phospholipid bilayers at the lipid-water interface. To this end, the steady-state fluorescence anisotropy, the differential polarized phase fluorometry, and the emission lifetime of the fluorophore were measured in isotropic ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00324a005
更新日期:1985-01-29 00:00:00
abstract::The key polyamine catabolizing enzyme spermidine-spermine N1-acetyltransferase (SSAT) is among the few genes known to be inducible by the natural polyamines. Certain polyamine analogs markedly exaggerate this response and thus provide useful tools for studying the underlying regulatory mechanisms. As shown here, the a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9612273
更新日期:1996-11-12 00:00:00
abstract::Oligomers of amyloid-β (Aβ) have emerged as the primary toxic agents responsible for early synaptic dysfunction and neuronal death in Alzheimer's disease (AD). Characterization of oligomers is an important step in the progress toward delineating the complex molecular mechanisms involved in AD pathogenesis. In our prev...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00161
更新日期:2016-04-19 00:00:00
abstract::The nonbulky 5',8-cyclopurine DNA lesions (cP) and the bulky, benzo[ a]pyrene diol epoxide-derived stereoisomeric cis- and trans- N2-guanine adducts (BPDE-dG) are good substrates of the human nucleotide excision repair (NER) mechanism. These DNA lesions were embedded at the In or Out rotational settings near the dyad ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b01066
更新日期:2019-02-12 00:00:00
abstract::The Escherichia coli single-strand binding (SSB) protein is an essential protein involved in DNA replication, recombination, and repair processes. The tetrameric protein binds to ss nucleic acids in a number of different binding modes in vitro. These modes differ in the number of nucleotides occluded per SSB tetramer ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00141a029
更新日期:1992-07-07 00:00:00
abstract::An antibody population that reacted with the high-affinity lysine binding site of human plasminogen was elicited by immunizing rabbits with an elastase degradation product containing kringles 1-3 (EDP I). This antibody was immunopurified by affinity chromatography on plasminogen-Sepharose and elution with 0.2 M 6-amin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00370a028
更新日期:1986-11-04 00:00:00
abstract::The catalytic activity of protein-tyrosine phosphatases (PTPs) is mediated by a cysteine side chain which carries out a nucleophilic attack initiating the phosphate cleavage. Experimentally, it has been observed that the active site cysteine has a remarkably low pKa. In the present study, we have investigated the orig...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971187i
更新日期:1998-04-21 00:00:00
abstract::The Cry1Ab toxin produced by Bacillus thuringiensis (Bt) exerts insecticidal action upon binding to BT-R1, a cadherin receptor localized in the midgut epithelium of the tobacco hornworm Manduca sexta [Dorsch, J. A., Candas, M., Griko, N. B., Maaty, W. S., Midboe, E. G., Vadlamudi, R. K., and Bulla, L. A., Jr. (2002) C...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700769s
更新日期:2007-09-04 00:00:00
abstract::As part of a larger effort to engineer the stability and hemin-binding properties of microsomal (Mc) cytochromes b(5) into rat liver outer mitochondrial membrane (OM) cytochrome (cyt) b(5), several mutants of rat OM cyt b(5) were prepared to study the effect of gradual and complete elimination of two extended hydropho...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi026005l
更新日期:2002-10-01 00:00:00
abstract::Glucose oxidation to CO2 was investigated in isolated perifused rat epididymal fat cells. Insulin stimulated rates of oxidation up to 30-fold. Multiple pulses of insulin or prolonged perifusion with the hormone led to a time-dependent desensitization of the cells. The action of insulin could be mimicked by H2O2. Rever...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00273a013
更新日期:1983-02-15 00:00:00
abstract::Ketosteroid isomerase (KSI) is one of the most proficient enzymes catalyzing an allylic isomerization reaction at a diffusion-controlled rate. In this study of KSI, we have detailed the structures of its active site, the role of various catalytic residues, and have explained the origin of the its fast reactivity by ca...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi001629h
更新日期:2000-11-14 00:00:00