Abstract:
:The vitamin K epoxide reductase (VKORC1) enzyme is of primary importance in many physiological processes, i.e., blood coagulation, energy metabolism, and arterial calcification prevention, due to its role in the vitamin K cycle. Indeed, VKORC1 catalyzes reduction of vitamin K epoxide to quinone and then to hydroquinone. However, the three-dimensional VKORC1 structure remains experimentally undetermined, because of the endoplasmic reticulum membrane location of this enzyme. Here we present a molecular modeling investigation of the VKORC1 enzymatic site structure and function, supported by in vitro enzymatic assays. Four VKORC1 mutants were designed in silico (F55G, F55Y, N80G, and F83G) based on a previous study that identified residues F55, N80, and F83 as being crucial for vitamin K epoxide binding. F55G, N80G, and F83G nonconservative mutants were all predicted to be inactive by molecular modeling analyses. However, the F55Y conservative mutant was expected to be active compared to wild-type VKORC1. In vitro enzymatic assays performed on recombinant proteins assessed our molecular modeling hypotheses and led us to describe the role of accurate VKORC1 active site residues with respect to VKORC1. Residues F55, N80, and F83 appeared to act in a concerted manner to keep vitamin K epoxide close to the C135 catalytic residue. Residues F55 and N80 prevent naphthoquinone head rotation away from the active site, assisted by residue F83 that prevents vitamin K from sliding outside the enzymatic pocket, through hydrophobic tail stabilization. Our results thus highlighted the specific functions of VKORC1 catalytic pocket residues and evidenced the ability of our structural model to predict biological effects of VKORC1 mutations.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Chatron N,Abi Khalil R,Benoit E,Lattard Vdoi
10.1021/acs.biochem.9b01084subject
Has Abstractpub_date
2020-04-07 00:00:00pages
1351-1360issue
13eissn
0006-2960issn
1520-4995journal_volume
59pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Exogenous mannosylphosphoryldolichol (Man-P-Dol) has previously been shown to stimulate UDP-GlcNAc:dolichyl phosphate N-acetylglucosamine 1-phosphate transferase (GPT1), the enzyme catalyzing the biosynthesis of N-acetylglucosaminylpyrophosphoryldolichol (GlcNAc-P-P-Dol). To define the structural specificity of the ma...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00200a036
更新日期:1994-08-30 00:00:00
abstract::The Stk1/Stp1 and GraSR signal-transduction pathways are two distinct pathways in Staphylococcus aureus that rely on a reversible phosphorylation process in transducing external stimuli intracellularly. Stk1/Stp1 is an eukaryote-like Ser/Thr kinase phosphatase pair involved in purine biosynthesis, cell-wall metabolism...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi401177n
更新日期:2013-11-12 00:00:00
abstract::A site-specific analog of ATP, 6,6'-dithiobis (inosinyl imidodiphosphate (S2P-PNP), inactivates the ATPase activities of myosin's proteolytic fragments, heavy meromyosin (HMM) and subfragment one (SF1), by formation of mixed disulfides between the 6 position of the purine ring and certain key cysteines. The stoichiome...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00680a015
更新日期:1975-05-06 00:00:00
abstract::While calcium binding to troponin C (TnC) triggers the contraction of both skeletal and cardiac muscle, there is clear evidence that different mechanisms may be involved. For example, activation of heart myofilaments occurs with binding to a single regulatory site on TnC, whereas activation of fast skeletal myofilamen...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971223d
更新日期:1997-10-07 00:00:00
abstract::High-resolution phosphorus-31 nuclear magnetic resonance (31P NMR) spectra of wild-type and mutant strains of Saccharomyces cerevisiae were observed at a frequency of 145.7 MHz. Levels of various phosphorus metabolites were investigated upon addition of glucose under both aerobic and anaerobic conditions. Three mutant...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00588a006
更新日期:1979-10-16 00:00:00
abstract::The triplet lifetime and absorption anisotropy decay of eosin-labeled band 3 was measured in resealed erythrocyte ghosts. Membrane potentials were generated by the addition of valinomycin in the presence of a K+ gradient. Neither negative nor positive membrane potentials had any detectable effect on the rotational dif...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00134a016
更新日期:1992-05-19 00:00:00
abstract::Detailed analysis of factors governing high affinity antibody-antigen interactions yields important insight into molecular recognition and facilitates the design of functional antibody libraries. Here we describe comprehensive mutagenesis of the light chain complementarity determining regions (CDRs) of HIV-1 antibody ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi100293q
更新日期:2010-07-06 00:00:00
abstract::The interaction of the Escherichia coli single-stranded DNA binding protein (SSB) with oligo- and poly-nucleotides has been studied by 270-MHz 1H NMR spectroscopy and fast kinetic techniques. d(pT)8 and poly(dT) were used to study noncooperative and cooperative binding, respectively. The H6, H1', and CH3 resonances of...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00320a036
更新日期:1984-12-04 00:00:00
abstract::Lysine side chains induce conformational changes in plasminogen (Pg) that regulate the process of fibrinolysis or blood clot dissolution. A lysine side-chain mimic, epsilon amino caproic acid (EACA), enhances the activation of Pg by urinary-type and tissue-type Pg activators but inhibits Pg activation induced by strep...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992028x
更新日期:2000-04-25 00:00:00
abstract::The structure and backbone dynamics of an extended second transmembrane segment (TM2e) of the human neuronal glycine receptor alpha(1) subunit in sodium dodecyl sulfate micelles were studied by (1)H and (15)N solution-state NMR. The 28-amino acid segment contained the consensus TM2 domain plus part of the linker betwe...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi026767g
更新日期:2003-04-08 00:00:00
abstract::A strategy to detect P-glycoprotein (P-gp) on cell membrane and quantify the cell number using electrochemical immunoassay was developed by effective surface immunoreactions and immobilization of cells on a highly hydrophilic interface, which was constructed by adsorption of colloidal gold nanoparticles on a methoxysi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0507332
更新日期:2005-08-30 00:00:00
abstract::Modification of pig kidney fructose-1,6-bisphosphatase with 2,3-butanedione in borate buffer (pH 7.8) leads to the loss of the activation of the enzyme by monovalent cations, as well as to the loss of allosteric adenosine 5'-monophosphate (AMP) inhibition. In agreement with the results obtained for the butanedione mod...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00661a017
更新日期:1976-08-10 00:00:00
abstract::Triplex-forming oligonucleotides (TFOs) have been shown to bind in a sequence-specific manner to polypurine/polypyrimidine sequences in several human gene promoters, including the c-myc P1 promoter. TFOs have been shown to inhibit transcription in vitro and the expression of target genes in cell culture. The human c-m...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00025a023
更新日期:1995-06-27 00:00:00
abstract::To study the substrate specificity and mechanism of thioltransferase (TTase) catalysis, we have used 14C- and 35S-radiolabeled mixed disulfides of cysteine and glutathione (GSH) with various cysteine-containing proteins. These protein mixed disulfide substrates were incubated with glutathione, glutathione disulfide (G...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00064a021
更新日期:1993-04-06 00:00:00
abstract::Our recently reported pressure-jump relaxation kinetics experiments on staphylococcal nuclease folding and unfolding [Vidugiris et al. (1995) Biochemistry 34, 4909] demonstrated that both transitions exhibit positive activation volumes, with that of folding being much larger than that of unfolding. Thus high pressure ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi952012g
更新日期:1996-03-26 00:00:00
abstract::6-[(4-Bromo-2,3-dioxobutyl)thio]-6-deaminoadenosine 5'-diphosphate (6-BDB-TADP) has been shown to react at the reduced diphosphopyridine nucleotide (DPNH) inhibitory site of bovine liver glutamate dehydrogenase with incorporation of 1 mol of reagent/mol of enzyme subunit [Batra, S. P., & Colman, R. F. (1984) Biochemis...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00360a005
更新日期:1986-06-17 00:00:00
abstract::The organization and interaction of chlorophylls (Chl) and the kinetics of the energy transfer in the core antenna of photosystem I (PSI) trimeric and monomeric complexes, isolated from Spirulina platensis with Triton X-100 have been studied by stationary and time-resolved fluorescence. At 295 K both complexes show an...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi970386z
更新日期:1997-11-11 00:00:00
abstract::Understanding the mechanisms of free energy transfer in metabolism is fundamental to understanding how the chemical forces that sustain the molecular organization of the cell are distributed. Recent studies of molecular motors (1-3) and ATP-driven proton transport (4-6) describe how chemical potential is transferred a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi025953j
更新日期:2002-07-02 00:00:00
abstract::Catalysis by glycogen phosphorylase involves a mechanism in which binding of one substrate tightens the binding of the other substrate to produce a productive ternary enzyme-substrate complex. In this work the molecular basis for this synergism is probed in crystallographic studies on ternary complexes in which the gl...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi960072w
更新日期:1996-06-11 00:00:00
abstract::The spontaneous hydrolyses of lactic acid O-phenyl phosphate (I) and, to a lesser extent, 3-hydroxybutyric acid O-phenyl phosphate (II) have been investigated and compared with similar intramolecular and bimolecular reactions. Compared to bimolecular nucleophilic reactions, the reactivity of II is similar to other sys...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00682a025
更新日期:1975-06-03 00:00:00
abstract::PEP mutase catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate in biosynthetic pathways leading to phosphonate secondary metabolites. A recent X-ray structure [Huang, K., Li, Z., Jia, Y., Dunaway-Mariano, D., and Herzberg, O. (1999) Structure (in press)] of the Mytilus edulis enzyme complexed wi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi990771j
更新日期:1999-10-26 00:00:00
abstract::Retinal membrane guanylyl cyclase (RetGC) in the outer segments of vertebrate photoreceptors is controlled by guanylyl cyclase activating proteins (GCAPs), responding to light-dependent changes of the intracellular Ca(2+) concentrations. We present evidence that a different RetGC binding protein, retinal degeneration ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi201342b
更新日期:2011-11-08 00:00:00
abstract::Several bifunctional alkylating agents of the aziridinylbenzoquinone class have been evaluated as potential antitumor agents. 3,6-Bis[(2-hydroxyethyl)amino]-2,5- diaziridinyl-1,4-benzoquinone (BZQ), 2,5-diaziridinyl-1,4-benzoquinone (DZQ), 3,6-bis(carboxyamino)-2,5-diaziridinyl- 1,4-benzoquinone (AZQ), and six analogu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00114a016
更新日期:1991-12-17 00:00:00
abstract::Previous studies of Escherichia coli dihydrofolate reductase (ecDHFR) have demonstrated that residue G121, which is 19 A from the catalytic center, is involved in catalysis, and long distance dynamical motions were implied. Specifically, the ecDHFR mutant G121V has been extensively studied by various experimental and ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0518242
更新日期:2006-02-07 00:00:00
abstract::Frequency-resolved fluorescence measurements have been performed to quantitate the lateral stress of the lipid layer containing nonbilayer phase preferring dioleoylphosphatidylethanolamine (DOPE). On the basis of a new rotational diffusion model, the wobbling diffusion constant (Dw), the curvature-related hopping diff...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00130a005
更新日期:1992-04-21 00:00:00
abstract::Human acidic mammalian chitinase (AMCase), a member of the family 18 glycosyl hydrolases, is one of the important proteins involved in Th2-mediated inflammation and has been implicated in asthma and allergic diseases. Inhibition of AMCase results in decreased airway inflammation and airway hyper-responsiveness in a mo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0525977
更新日期:2006-04-11 00:00:00
abstract::Human DNA primase synthesizes short RNA primers that DNA polymerase alpha then elongates during the initiation of all new DNA strands. Even though primase misincorporates NTPs at a relatively high frequency, this likely does not impact the final DNA product since the RNA primer is replaced with DNA. We used an extensi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9019516
更新日期:2010-02-02 00:00:00
abstract::The R2 protein of ribonucleotide reductase catalyzes the dioxygen-dependent one-electron oxidation of Tyr122 at a diiron-carboxylate site. Methane monooxygenase and related hydroxylases catalyze hydrocarbon hydroxylation at diiron sites structurally related to the one in R2. In protein R2, the likely reaction site for...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9806403
更新日期:1998-07-28 00:00:00
abstract::The transformation of DMPC vesicles containing myristic acid to larger structures was examined by nuclear magnetic resonance techniques. The process was found to be characterized by a rate which is approximately first order in vesicle concentration. Rates, however, show a dramatic increase with increasing myristic aci...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00610a027
更新日期:1978-08-22 00:00:00
abstract::The repeating units of mouse, rat, and alpha-monkey satellites have been cloned. All three show properties that are characteristic of curved DNA: (i) their migration in polyacrylamide gels is slower than predicted from their sequences, and (ii) they appear as curved molecules when visualized by electron microscopy. Al...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00461a019
更新日期:1990-03-06 00:00:00