Abstract:
:Human DNA is continuously damaged by exogenous and endogenous genotoxic insults. To counteract DNA damage and ensure the completion of DNA replication, cells possess specialized DNA polymerases (Pols) that bypass a variety of DNA lesions. Human DNA polymerase kappa (hPolkappa) is a member of the Y-family of DNA Pols and a direct counterpart of DinB in Escherichia coli. hPolkappa is characterized by its ability to bypass several DNA adducts [e.g., benzo[a]pyrene diolepoxide-N(2)-deoxyguanine (BPDE-N(2)-dG) and thymine glycol] and efficiently extend primers with mismatches at the termini. hPolkappa is structurally distinct from E. coli DinB in that it possesses an approximately 100-amino acid extension at the N-terminus. Here, we report that tyrosine 112 (Y112), the steric gate amino acid of hPolkappa, which distinguishes dNTPs from rNTPs by sensing the 2'-hydroxy group of incoming nucleotides, plays a crucial role in extension reactions with mismatched primer termini. When Y112 was replaced with alanine, the amino acid change severely reduced the catalytic constant, i.e., k(cat), of the extending mismatched primers and lowered the efficiency, i.e., k(cat)/K(m), of this process by approximately 400-fold compared with that of the wild-type enzyme. In contrast, the amino acid replacement did not reduce the insertion efficiency of dCMP opposite BPDE-N(2)-dG in template DNA, nor did it affect the ability of hPolkappa to bind strongly to template-primer DNA with BPDE-N(2)-dG/dCMP. We conclude that the steric gate of hPolkappa is a major fidelity factor that regulates extension reactions from mismatched primer termini.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Niimi N,Sassa A,Katafuchi A,Grúz P,Fujimoto H,Bonala RR,Johnson F,Ohta T,Nohmi Tdoi
10.1021/bi900153tsubject
Has Abstractpub_date
2009-05-26 00:00:00pages
4239-46issue
20eissn
0006-2960issn
1520-4995journal_volume
48pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Rhodobacter sphaeroides strains lacking cytochrome c2 (cyt c2), the normal electron donor to P870+ in light-oxidized reaction center (RC) complexes, are unable to grow photosynthetically. However, spd mutations that suppress the photosynthetic deficiency of cyt c2 mutants elevate levels of the cyt c2 isoform, isocyt c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi961648k
更新日期:1997-01-28 00:00:00
abstract::Whole tRNA preparation obtained from a human cell line (HT-29) of colon carcinoma and purified specific Escherichia coli tRNA were reacted with pyridoxal 5'-phosphate, reduced by sodium borohydride and digested with RNase A and snake venom phosphodiesterase. Two-dimensional chromatography of the pyridoxal 5'-phosphate...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00635a033
更新日期:1977-08-09 00:00:00
abstract::Indolotryptoline natural products represent a small family of structurally unique chromopyrrolic acid-derived antiproliferative agents. Like many prospective anticancer agents before them, the exploration of their potential clinical utility has been hindered by the limited information known about their mechanism of ac...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi501078j
更新日期:2014-11-18 00:00:00
abstract::Staphylococcus aureus transcription factor QacR regulates expression of the qacA multidrug efflux determinant. In response to binding cationic lipophilic compounds, including ethidium and rhodamine 6G, QacR dissociates from the qacA operator alleviating repression. Such ligand binding uniformly induces a coil-to-helix...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi901102h
更新日期:2009-10-20 00:00:00
abstract::Efforts to elucidate the nature of the bimolecular interaction of parathyroid hormone (PTH) with its cognate receptor, the PTH receptor type 1 (PTHR1), have relied heavily on benzoylphenylalanine- (Bpa-) based photoaffinity cross-linking. However, given the flexibility, size, and shape of Bpa, the resolution at the PT...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi800122f
更新日期:2008-06-03 00:00:00
abstract::Ca2+-free crystals of sarcoplasmic reticulum Ca2+-ATPase have, up until now, been obtained in the presence of inhibitors such as thapsigargin (TG), bound to the transmembrane region of this protein. Here, we examined the consequences of such binding for the protein. We found that, after TG binding, an active site liga...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi701855r
更新日期:2007-12-25 00:00:00
abstract::Chorismate mutase catalyzes the first committed step toward the biosynthesis of the aromatic amino acids, phenylalanine and tyrosine. While this biosynthetic pathway exists exclusively in the cell cytoplasm, the Mycobacterium tuberculosis enzyme has been shown to be secreted into the extracellular medium. The secretor...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0606445
更新日期:2006-06-13 00:00:00
abstract::A procedure has been developed to purify foot and mouth disease virus (FMDV) VP1 surface antigens from recombinant Escherichia coli. The VP1 antigens are expressed as fusion proteins derived from the E. coli Trp operon and VP1 surface protein of FMDV. The procedure is capable of recovering greater than 96% of the desi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00321a031
更新日期:1984-12-18 00:00:00
abstract::We have determined the fidelity of in vitro DNA synthesis catalyzed at high temperature by the DNA polymerase from the thermophilic bacterium Thermus aquaticus. Using a DNA substrate that contains a 3'-OH terminal mismatch, we demonstrate that the purified polymerase lacks detectable exonucleolytic proofreading activi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00416a027
更新日期:1988-08-09 00:00:00
abstract::Carbamoylation and reductive methylation of tubulin have been shown previously to inhibit microtubule assembly, probably by attack on essential internal lysine residues [Mellado, W., Slebe, J., & Maccioni, R.B. (1982) Biochem. J. 203, 675-681; Szasz, J., Burns, R., & Sternlicht, H. (1982) J. Biol. Chem. 257, 3697-3704...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00403a027
更新日期:1988-02-09 00:00:00
abstract::SHAPE-MaP is unique among RNA structure probing strategies in that it both measures flexibility at single-nucleotide resolution and quantifies the uncertainties in these measurements. We report a straightforward analytical framework that incorporates these uncertainties to allow detection of RNA structural differences...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b00977
更新日期:2015-11-24 00:00:00
abstract::In cerebellum, inositol trisphosphate- (InsP(3)-) gated Ca channels play a key role in learning, though they exhibit a low sensitivity to InsP(3) compared to peripheral tissues. In the present study, the cerebellar InsP(3) receptor is shown to be associated with a novel inhibitor of InsP(3) binding. (3)H-InsP(3) bindi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992175v
更新日期:2000-03-28 00:00:00
abstract::F0F1 ATP synthase harnesses a transmembrane electrochemical gradient for the production of ATP. When operated in reverse, this multiprotein complex catalyzes ATP hydrolysis. In bacteria, the ε subunit is involved in regulating this ATPase activity. Also, ε is essential for coupling ATP hydrolysis (or synthesis) to pro...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi5004684
更新日期:2014-06-24 00:00:00
abstract::The complete primary structure of the major component myoglobin from the Arctic minke whale, Balaenoptera acutorostrata, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. Over 80% of the amino acid sequence was established from the three ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00623a023
更新日期:1977-02-22 00:00:00
abstract::Platelet receptor recognition domains are located on the gamma and alpha chains of human fibrinogen. The former encompasses residues 400-411 [Kloczewiak, M., Timmons, S., Lukas, T. J., & Hawiger, J. (1984) Biochemistry 23, 1767], and the latter is present in two loci on the alpha chain (alpha 95-97 and alpha 572-574) ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00433a026
更新日期:1989-04-04 00:00:00
abstract::The chemical shifts of all the aromatic proton and anomeric proton resonances of NADP+, NADPH, and several structural analogues have been determined in their complexes with Lactobacillus casei dihydrofolate reductase by double-resonance (saturation transfer) experiments. The binding of NADP+ to the enzyme leads to lar...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00557a015
更新日期:1980-08-05 00:00:00
abstract::Tropomyosin is postulated to confer stability to actin filaments in nonmuscle cells. We have found that a nonmuscle tropomyosin isolated from the intestinal epithelium can directly stabilize actin filaments by slowing depolymerization from the pointed, or slow-growing, filament end. Kinetics of elongation and depolyme...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00447a035
更新日期:1989-10-17 00:00:00
abstract::Mutation of Gly90, Glu113, Ala292, and Lys296 in the visual pigment rhodopsin constitutively activates the protein for activation of the G protein transducin. Three of these mutations have been shown to cause two different human diseases. Mutation of Gly90 and Ala292 results in complete night blindness, and mutation o...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00037a035
更新日期:1995-09-19 00:00:00
abstract::Oxidized cytochrome c oxidase exists in two reasonably well-defined conformations, a high-spin conformation with maximal absorption at 418 nm and a low-spin conformation with maximal absorption at 428 nm. The equilibrium between these two conformations has been studied as a function of pH, pressure, and temperature. p...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00265a009
更新日期:1982-10-26 00:00:00
abstract::The amino acid sequence of human alpha-fetoprotein, a 67-kDa protein present in mammalian embryonic serum, was verified by fast atom bombardment mass spectrometric (FAB/MS) analyses of three different enzymatic digests of the protein. Human alpha-fetoprotein obtained from a large-scale cell culture was digested with t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00234a032
更新日期:1991-05-21 00:00:00
abstract::Nickel is a fundamental micronutrient for cellular life, but it is toxic in soluble form at nonphysiological concentrations. Such potentially contradictory features required living organisms to develop efficient systems for nickel utilization and homeostasis. This is the case for incorporation of nickel into the activ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi6024676
更新日期:2007-03-20 00:00:00
abstract::In the ATP-dependent carboxylation of biotin that is catalyzed by most biotin-dependent carboxylases, a fundamental mechanistic question is whether the ATP activates bicarbonate (via the formation of carboxyphosphate as an intermediate) or whether the ATP activates biotin (via the formation of O-phosphobiotin). We hav...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00421a009
更新日期:1988-10-18 00:00:00
abstract::Efforts toward the development of RNA-based drug leads have been challenging because of the complexity and dynamic nature of RNA structures as therapeutic targets. The transactivation response (TAR) RNA and cognate Tat protein of HIV have long been recognized as promising antiviral targets, and recent works have ident...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b00325
更新日期:2015-06-16 00:00:00
abstract::The proton nuclear Overhauser effects of bovine alpha-lactalbumin were studied at 200 MHz by irradiation of an upfield ring current shifted methylene at -2.45 ppm (assigned to Ile-95) and two aromatic protons, Tyr-103 (8.36 ppm) and Trp-60 (5.85 ppm). The experimental results were consistent with a putative three-dime...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00346a035
更新日期:1985-12-03 00:00:00
abstract::Biotin synthase, the enzyme which catalyzes the last step of the biosynthesis of biotin, contains only (2Fe-2S)(2+) clusters when isolated under aerobic conditions. Previous results showed that reduction by dithionite or photoreduced deazaflavin converts the (2Fe-2S)(2+) to (4Fe-4S)(2+,+). However, until now, no detai...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi034426c
更新日期:2003-07-29 00:00:00
abstract::Cytochrome P-450(M-1) [P-450(M-1)] is specifically expressed in adult male rat liver [Yoshioka, H., Morohashi, K., Sogawa, K., Miyata, T., Kawajiri, K., Hirose, T., Inayama, S., Fujii-Kuriyama, Y., & Omura, T. (1987) J. Biol. Chem. 262, 1706-1711]. Isolation and analysis of the gene for P-450(M-1) revealed that the co...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00399a039
更新日期:1987-12-15 00:00:00
abstract::Xylose isomerase (E.C. 5.3.1.5) catalyzes the interconversion of aldose and ketose sugars and has an absolute requirement for two divalent cations at its active site to drive the hydride transfer rates of sugar isomerization. Evidence suggests some degree of metal movement at the second metal site, although how this m...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi049812o
更新日期:2004-06-01 00:00:00
abstract::Heme (iron protoporphyrin IX) is an essential protein prosthetic group and signaling molecule required for most life on Earth. All heme-dependent processes require the dynamic and rapid mobilization of heme from sites of synthesis or uptake to hemoproteins present in virtually every subcellular compartment. The cytoto...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.7b00007
更新日期:2017-04-04 00:00:00
abstract::When partially purified Ehrlich ascites tumor RNA polymerase II was further purified on a column of phosphocellulose, stimulation of its catalysis of RNA synthesis by stimulatory factor S-II was greatly decreased. This decrease in sensitivity to the stimulatory factor was reversible: the enzyme eluted from phosphocell...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00645a006
更新日期:1977-12-27 00:00:00
abstract::Inosine has the ability to act as a "wild-card" binding nonspecifically to both A.T and G.C base pairs. This has obvious implications for the design of oligonucleotide site-directed probes. In this paper we present a series of oligonucleotides with a 5'pur9-pyr9-pyr9 motif which are designed to fold up sequentially in...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi960193w
更新日期:1996-10-15 00:00:00