Abstract：
:The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and γ-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the β-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino-acid residues for the catalysis of adenylate kinase.
journal_name
J Biochemjournal_title
Journal of biochemistryauthors
Shibanuma Y,Nemoto N,Yamamoto N,Sampei GI,Kawai Gdoi
10.1093/jb/mvaa043subject
Has Abstractpub_date
2020-09-01 00:00:00pages
223-229issue
3eissn
0021-924Xissn
1756-2651pii
5818497journal_volume
168pub_type
杂志文章abstract：:The mobility of spin labels covalently bound to the Ca2+-transport ATPase (ATP phosphohydrolase [EC 3.y.1.3]) was studied by electron spin-resonance spectroscopy in purified ATPase and reconstituted vesicles. The purified ATPase of sarcoplasmic reticulum of rabbit skeletal muscle was covalently labeled with maleimide ...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a133183
更新日期：1981-01-01 00:00:00
abstract：:The stress-related protein Stm1 interacts with ribosomes, and is implicated in repressing translation. Stm1 was previously studied both in vivo and in vitro by cell-free translation systems using crude yeast lysates, but its precise functional mechanism remains obscure. Using an in vitro reconstituted translation syst...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/jb/mvx070
更新日期：2018-03-01 00:00:00
abstract：:Genomic clones of UDP-glucuronosyltransferase family 1 (UGT1) were isolated from wild-type Wistar rats. The UGT1 locus spans > 120 kb and forms a gene complex. In this locus nine unique first exons encoding NH2-terminal portions of each isoform were located at intervals of approximately 10 kb and followed by only one ...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/jb/117.2.392
更新日期：1995-02-01 00:00:00
abstract：:Using a new cannulation method, which completely prevented interruption of circulation to brain tissue during surgical operations, we could prepare a functionally intact hemoglobin-free isolated perfused rat head in situ. The frequency distribution (8-25 Hz) and amplitude of a spontaneous electroencephalogram, EEG (50...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a124098
更新日期：1993-06-01 00:00:00
abstract：:Cathepsin E (CE) is an intracellular aspartic proteinase that is exclusively expressed in cells of the gastrointestinal tracts, lymphoid tissues, urinary organs and red blood cells. However, the molecular mechanism by which CE is predominantly expressed in these cells remains unknown. Here, we report the identificatio...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/jb/mvr135
更新日期：2012-03-01 00:00:00
abstract：:Fluorescence resonance energy transfer spectroscopy has been used to study the spatial relationships between probes attached to actin and troponin in the reconstituted skeletal muscle thin filament in the presence and absence of Ca2+ ions. Gln-41 and the nucleotide-binding site of actin were selectively labeled with t...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a021940
更新日期：1998-02-01 00:00:00
abstract：:Chicken liver mitochondria contained two forms of phosphoenolpyruvate (PEP) carboxykinase (designated as Mt-I and Mt-II) and the chicken liver cytosol fraction contained three forms of PEP carboxykinase (designated as Sol-I, Sol-II, and Sol-III). Mt-I and Mt-II were purified to homogeneity. They both had a molecular w...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a133045
更新日期：1980-09-01 00:00:00
abstract：:A high molecular weight protease inhibitor was purified from the egg white of Cuban crocodile (Crocodylus rhombifer). It inhibited the casein hydrolyzing activity of trypsin, subtilisin and papain. Its native molecular weight was 730,000 and it consisted of four subunits of equal molecular weight, each pair of which w...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a134145
更新日期：1983-01-01 00:00:00
abstract：:An anti-oxygen radical reagent of a bacterial metabolite, M874 monogalactoglycerolipid (di-O-12-methyl-tetradecanoyl-3-O-beta-D-galactopyranosyl-sn-glycerol ), was tested for its ability to protect two organisms against cellular lesions induced by 5-aminolevulinic acid (ALA) and light. In Corynebacterium flavescens AT...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a022674
更新日期：2000-05-01 00:00:00
abstract：:Hydrostatic pressure-induced morphological and physiochemical changes in monomeric myosin were investigated. The turbidity of a myosin solution increased after release of pressure, indicating aggregation of the molecules. Some molecules were single headed after exposure to 100-200 MPa, in contrast with an intact molec...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a124496
更新日期：1994-07-01 00:00:00
abstract：:A cDNA clone inducible by either a tumor promoter, 12-o-tetradecanoyl phorbol-13-acetate (TPA), or a T-cell mitogen, phytohemagglutinin (PHA), was isolated from a cDNA library constructed from the poly(A) + RNAs of TPA- and PHA-stimulated human tonsillar lymphocytes, and was named pLD78. Stimulation of the tonsillar l...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a135549
更新日期：1986-03-01 00:00:00
abstract：:The cellular Src (c-Src) tyrosine kinase is upregulated and believed to play a pivotal role in various human cancers. However, the molecular mechanism underlying c-Src-mediated tumour progression remains elusive. Recent studies have revealed that several microRNAs (miRNAs) function as tumour suppressors by regulating ...
journal_title：Journal of biochemistry
pub_type： 杂志文章,评审
doi：10.1093/jb/mvv036
更新日期：2015-06-01 00:00:00
abstract：:Administration of an excessive dose of Bacillus subtilis alpha-amylase [EC 3.2.1.1, alpha-1,4-glucan 4-glucanohydrolase] (BalphaA) induced the production of non-precipitating (non-ppt) IgG2 antibody in guinea pigs, whereas immunization with a normal dose produced precipitating (ppt) IgG1 and IgG2 antibodies. The non-p...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a131657
更新日期：1977-07-01 00:00:00
abstract：:Sialoglycoprotein which exhibits inhibitory activity for hemagglutination by Hemagglutinating Virus of Japan (HVJ, Sendai virus) was isolated from the membrane of bovine erythrocytes. Purification steps for this sialoglycoprotein included extraction with lithium diiodosalicylate, phenol partition, precipitation with e...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a134301
更新日期：1983-06-01 00:00:00
abstract：:Protein phosphorylation is a key regulatory mechanism of the organization and dynamics of the actin cytoskeleton during cell motility, differentiation, and cytokinesis. The level of protein phosphorylation is dependent on the relative activities of both protein kinases and protein phosphatases. In this paper, we exami...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a022375
更新日期：1999-05-01 00:00:00
abstract：:The sugar chain of bovine pancreatic ribonuclease B was released from the polypeptide moiety by hydrazinolysis and by endo-beta-N-acetylglucosaminidase H digestion, and reduced with NaB[3H]4 after N-acetylation. The radioactive oligosaccharide mixtures thus obtained were fractionated by Bio-Gel P-4 column chromatograp...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：
更新日期：1980-07-01 00:00:00
abstract：:Actin-microtubule crosstalk is implicated in the formation of cellular protrusions, but the mechanism remains unclear. In this study, we examined the regulation of cell protrusion involving a ubiquitously expressed microtubule-associated protein (MAP) 4, and its superfamily proteins, neuronal MAP2 and tau. Fluorescenc...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/jb/mvaa046
更新日期：2020-09-01 00:00:00
abstract：:Partial amino acid sequences of two mitochondrial cytochrome P-450's, P-450 (SCC) and P-450 (11 beta), and two microsomal cytochrome P-450's, P-450 (C-21), and P-450 (17 alpha, Lyase), from adrenal cortex were analyzed and compared. Mitochondrial P-450's and microsomal P-450's were different in the amino acid sequence...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：
更新日期：1983-11-01 00:00:00
abstract：:Escherichia coli spr (suppressor of prc) mutants and nlpI mutants show thermosensitive growth. The thermosensitivity of the spr mutants was suppressed by the nlpI mutations. Expression of the fusion genes encoding hexa-histidine-tagged NlpI (NlpI-His) and purification of the tagged NlpI showed that NlpI-His bound with...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/jb/mvh022
更新日期：2004-02-01 00:00:00
abstract：:An inhibitor of blood coagulation, a new protein with an apparent molecular weight of 34,000 and an isoelectric point of 4.9, was purified from human placental tissue by EDTA extraction. Five cDNA clones were isolated from the human placental lambda gt11 cDNA library using the mouse monoclonal antibody raised against ...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a122165
更新日期：1987-11-01 00:00:00
abstract：:Resistant strains for trimethoprim, a potent inhibitor of dihydrofolate reductase, were obtained by transforming the ligated products of Escherichia coli K12 DNA and plasmid pBR322 BamH I fragments. The strains carry a 13.6 kbp plasmid, pTP1, which contains the trimethoprim- and ampicillin-resistance determinant genes...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a133804
更新日期：1982-04-01 00:00:00
abstract：:The fluorometric method of Nash for determination of methanol was applied in assay of kallikrein-like arginine esterases using N-a-tosyl-L-arginine methyl ester (TAME) as substrate. The results obtained using this method corresponded well with those obtained in the usual colorimetric methods using hydroxamate, chromot...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a131174
更新日期：1976-06-01 00:00:00
abstract：:The phospholipid mediator, platelet activating factor (PAF: 1-O-alkyl-2-O-acetyl-sn-glycero-3-phosphocholine), was recently reported to activate macrophage-monocyte cells as well as neutrophils or platelets. PAF was incorporated into dipalmitoylphosphatidylcholine-cholesterol liposomes, and their effect on guinea pig ...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a135172
更新日期：1985-04-01 00:00:00
abstract：:It has been reported that two kinds of Cd-binding peptide (Cd-BP1 and Cd-BP2) are induced in fission yeast upon exposure to Cd, and that they consist of the same unit peptide (cadystin), but Cd-BP1 binds 1.5 times more Cd atoms per cadystin than Cd-BP2 (Murasugi, A., Wada, C., & Hayashi, Y. (1981) J. Biochem. 90, 1561...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a134965
更新日期：1984-11-01 00:00:00
abstract：:1) Two forms of acid beta-galactosidase [EC 3.1.23] with different molecular weights catalyzing the hydrolysis of GM1-ganglioside and p-nitrophenyl-beta-D-galactoside were separated and purified from porcine spleen. 2) The apparent molecular weights were 400,000-600,000 and 70,000-74,000 for the high (termed Am form) ...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a133910
更新日期：1982-07-01 00:00:00
abstract：:We report a strategy for generating efficient signal transduction with unnatural heterologous receptor combinations. As previously described [Ueda, H., Kawahara, M. et al. (2000) J. Immunol. Methods 241, 159-170], chimeric receptors composed of the V(H)/V(L) domains of anti-hen egg lysozyme antibody HyHEL-10 and N-ter...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a002987
更新日期：2001-08-01 00:00:00
abstract：:The kinetics of the hydrogen-deuterium exchange reaction in sarcoplasmic reticulum (SR) membranes isolated from rabbit skeletal muscle was followed by infrared absorption measurements. The exchange rate in SR was much lower than that in the soluble proteins reported so far. When adenylyl-imidophosphate (AMPPNP, an TP ...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a133480
更新日期：1981-08-01 00:00:00
abstract：:It has been reported that neutral salts such as NaCl activate the thermolysin-catalyzed hydrolysis of substrates containing glycine at the P1 position (carboxylic side of the cleavage bond) [Holmquist, B. & Vallee, B.L. (1976) Biochemistry 15, 101-107]. In this paper, we demonstrate that high concentrations (1-4 M) of...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a123901
更新日期：1992-09-01 00:00:00
abstract：:Histidinoalanine, a cross-linking component of connective tissue proteins, was detected in the acid hydrolysate of human urine. The concentrations in urines from newborn babies, children, and adults were 1.33 +/- 0.27, 0.77 +/- 0.23, and 0.89 +/- 0.33 nmol/mg creatinine, respectively. Possible origins of urinary histi...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a121774
更新日期：1986-09-01 00:00:00
abstract：:The nucleotide sequence of the aspartate aminotransferase [EC 2.6.1.1] structural gene, aspC, of Escherichia coli K-12 was determined. The coding region of the aspC gene contained 1,188 nucleotide residues and encoded 396 amino acid residues. The amino acid sequence deduced from the nucleotide sequence agreed perfectl...
journal_title：Journal of biochemistry
pub_type： 杂志文章
doi：10.1093/oxfordjournals.jbchem.a135173
更新日期：1985-04-01 00:00:00
