P450cam visits an open conformation in the absence of substrate.

Abstract:

:P450cam from Pseudomonas putida is the best characterized member of the vast family of cytochrome P450s, and it has long been believed to have a more rigid and closed active site relative to other P450s. Here we report X-ray structures of P450cam crystallized in the absence of substrate and at high and low [K(+)]. The camphor-free structures are observed in a distinct open conformation characterized by a water-filled channel created by the retraction of the F and G helices, disorder of the B' helix, and loss of the K(+) binding site. Crystallization in the presence of K(+) alone does not alter the open conformation, while crystallization with camphor alone is sufficient for closure of the channel. Soaking crystals of the open conformation in excess camphor does not promote camphor binding or closure, suggesting resistance to conformational change by the crystal lattice. This open conformation is remarkably similar to that seen upon binding large tethered substrates, showing that it is not the result of a perturbation by the ligand. Redissolved crystals of the open conformation are observed as a mixture of P420 and P450 forms, which is converted to the P450 form upon addition of camphor and K(+). These data reveal that P450cam can dynamically visit an open conformation that allows access to the deeply buried active site without being induced by substrate or ligand.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Lee YT,Wilson RF,Rupniewski I,Goodin DB

doi

10.1021/bi100183g

subject

Has Abstract

pub_date

2010-04-27 00:00:00

pages

3412-9

issue

16

eissn

0006-2960

issn

1520-4995

journal_volume

49

pub_type

杂志文章
  • Time-dependent inhibition of Bacillus stearothermophilus alanine racemase by (1-aminoethyl)phosphonate isomers by isomerization to noncovalent slowly dissociating enzyme-(1-aminoethyl)phosphonate complexes.

    abstract::An alanine racemase encoded by a gene from the thermophilic Gram-positive bacterium Bacillus stearothermophilus is overproduced to 0.3% of the soluble protein when carried on plasmid pICR4 in Escherichia coli [Inagaki, K., Tanizawa, K., Badet, B., Walsh, C. T., Tanaka, H., & Soda, K. (1986) Biochemistry (third paper o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00359a029

    authors: Badet B,Inagaki K,Soda K,Walsh CT

    更新日期:1986-06-03 00:00:00

  • Calorimetric detection of influenza virus induced membrane fusion.

    abstract::Membrane fusion induced by the hemagglutinin glycoprotein of influenza virus has been extensively characterized, but the mechanism whereby the protein achieves the merger of the viral and target membrane lipids remains enigmatic. Various lipid intermediate structures have been proposed, and the energies required for t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00017a001

    authors: Nebel S,Bartoldus I,Stegmann T

    更新日期:1995-05-02 00:00:00

  • 13C, 15N, and 31P NMR studies on 6-hydroxy-L-nicotine oxidase from Arthrobacter oxidans.

    abstract::The interaction between the apoprotein of 6-hydroxy-L-nicotine oxidase from Arthrobacter oxidans and the prosthetic group FAD has been investigated by 13C, 15N, and 31P NMR techniques. The FAD prosthetic group was selectively enriched in 13C and 15N isotopes by adding isotopically labeled riboflavin derivatives to the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00428a016

    authors: Pust S,Vervoort J,Decker K,Bacher A,Müller F

    更新日期:1989-01-24 00:00:00

  • Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A.

    abstract::X-ray crystallographic data to 1.9-A resolution were collected on sperm whale metmyoglobin equilibrated with 7 atm of xenon gas. The results indicate four xenon sites of occupancy from 0.45 to 1.0. These sites are located in interior spaces or packing defects of the myoglobin molecule. The effects of the bound xenon o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00308a002

    authors: Tilton RF Jr,Kuntz ID Jr,Petsko GA

    更新日期:1984-06-19 00:00:00

  • Fluorescence energy transfer between Ca2+ transport ATPase molecules in artificial membranes.

    abstract::The purified ATPase of sarcoplasmic reticulum was covalently labeled with N-iodoacetyl-N'-(5-sulfo-1-naphthyl)ethylenediamine (1,5-IAEDANS) or with iodoacetamidofluorescein (IAF). In reconstituted vesicles containing both types of ATPase molecules fluorescence energy transfer was observed from the IAEDANS (donor) to t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00626a003

    authors: Vanderkooi JM,Ierokomas A,Nakamura H,Martonosi A

    更新日期:1977-04-05 00:00:00

  • Subtle Dynamic Changes Accompany Hck Activation by HIV-1 Nef and are Reversed by an Antiretroviral Kinase Inhibitor.

    abstract::The HIV-1 virulence factor Nef interacts with the macrophage Src-family kinase Hck, resulting in constitutive kinase activation that contributes to viral replication and immune escape. Previous chemical library screens identified the diphenylfuranopyrimdine kinase inhibitor DFP-4AB, which selectively inhibits Nef-depe...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00875

    authors: Wales TE,Hochrein JM,Morgan CR,Emert-Sedlak LA,Smithgall TE,Engen JR

    更新日期:2015-10-20 00:00:00

  • The application of 0.1 M quadrol to the microsequence of proteins and the sequence of tryptic peptides.

    abstract::In an effort to extend automated Edman degradation to nanomole quantities of protein, the method of sequenator analysis described by Edman and Begg (Edman, P., and Begg, G. (1967), Eur. J. Biochem. 1, 80) was modified to permit long degradations in the absence of carrier proteins. By using an aqueous 0.1 M Quadrol pro...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00684a036

    authors: Brauer AW,Margolies MN,Haber E

    更新日期:1975-07-01 00:00:00

  • Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function.

    abstract::Thiolases are CoA-dependent enzymes which catalyze the formation of a carbon-carbon bond in a Claisen condensation step and its reverse reaction via a thiolytic degradation mechanism. Mitochondrial acetoacetyl-coenzyme A (CoA) thiolase (T2) is important in the pathways for the synthesis and degradation of ketone bodie...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi6026192

    authors: Haapalainen AM,Meriläinen G,Pirilä PL,Kondo N,Fukao T,Wierenga RK

    更新日期:2007-04-10 00:00:00

  • Analysis of substrate-induced electronic, catalytic, and structural changes in inducible NO synthase.

    abstract::Inducible nitric oxide synthase (iNOS) catalyzes the NADPH-dependent formation of nitric oxide (NO) and citrulline from L-arginine and O2. In addition to serving as substrate, L-arginine alters the enzyme's heme iron spin equilibrium, increases its NADPH oxidation, and promotes assembly of active dimeric iNOS from ina...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi952844e

    authors: Sennequier N,Stuehr DJ

    更新日期:1996-05-07 00:00:00

  • Functional compensation of a recognition-defective transfer RNA by a distal base pair substitution.

    abstract::A single G3:U70 base pair in the acceptor helix is the major determinant of alanine acceptance in alanine transfer RNAs. Transfer of this base pair into other transfer RNAs confers alanine acceptance. A G3:C70 substitution eliminates alanine acceptance in vivo and in vitro. In this work, a population of mutagenized G3...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00157a019

    authors: Hou YM,Schimmel P

    更新日期:1992-10-27 00:00:00

  • NMR study of nitrogen-15-labeled Escherichia coli valine transfer RNA.

    abstract::1,3-15N-Labeled uracil was synthesized chemically and used to prepare labeled Escherichia coli tRNA(Val) biosynthetically. 500-MHz measurements of 15N and proton chemical shift were obtained, for all uridine and uridine-related bases, by heteronuclear multiple-quantum coherence spectroscopy. All the uracil NH group re...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00166a013

    authors: Choi BS,Redfield AG

    更新日期:1992-12-29 00:00:00

  • Hemagglutinins from two influenza virus variants bind to sialic acid derivatives with millimolar dissociation constants: a 500-MHz proton nuclear magnetic resonance study.

    abstract::The equilibrium binding of influenza virus hemagglutinin to derivatives of its cell-surface ligand, sialic acid, was measured by nuclear magnetic resonance (NMR) spectroscopy. Binding was quantified by observing perturbations of sialic acid resonances in the presence of protein. The major perturbation observed was a c...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00447a018

    authors: Sauter NK,Bednarski MD,Wurzburg BA,Hanson JE,Whitesides GM,Skehel JJ,Wiley DC

    更新日期:1989-10-17 00:00:00

  • Proximity of periplasmic loops in the lactose permease of Escherichia coli determined by site-directed cross-linking.

    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

    authors: Sun J,Kaback HR

    更新日期:1997-09-30 00:00:00

  • Glycosylated polyproline II rods with kinks as a structural motif in plant hydroxyproline-rich glycoproteins.

    abstract::Hydroxyproline-rich glycoproteins (HRGPs) are the major proteinaceous components of higher plant walls and the predominant components of the cell wall of the green alga Chlamydomonas reinhardtii. The GP1 protein, an HRGP of the C. reinhardtii wall, is shown to adopt a polyproline II helical configuration and to carry ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0023605

    authors: Ferris PJ,Woessner JP,Waffenschmidt S,Kilz S,Drees J,Goodenough UW

    更新日期:2001-03-06 00:00:00

  • FIONA on Caenorhabditis elegans.

    abstract::Despite much work, subcellular neurons of Caenorhabditis elegans have not been studied at nanometer resolution with millisecond time resolution. Nor has there been an effective way to immobilize C. elegans. Here we show that, without using anesthetic or paralyzing agents, fluorescence imaging with one-nanometer accura...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi8023477

    authors: Kural C,Nonet ML,Selvin PR

    更新日期:2009-06-09 00:00:00

  • Intestinal absorption of dietary cholesteryl ester is decreased but retinyl ester absorption is normal in carboxyl ester lipase knockout mice.

    abstract::Carboxyl ester lipase (CEL; EC 3.1.1.13) hydrolyzes cholesteryl esters and retinyl esters in vitro. In vivo, pancreatic CEL is thought to liberate cholesterol and retinol from their esters prior to absorption in the intestine. CEL is also a major lipase in the breast milk of many mammals, including humans and mice, an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi981679a

    authors: Weng W,Li L,van Bennekum AM,Potter SH,Harrison EH,Blaner WS,Breslow JL,Fisher EA

    更新日期:1999-03-30 00:00:00

  • An atomic-level mechanism for molybdenum nitrogenase. Part 1. Reduction of dinitrogen.

    abstract::The properties of the Fe and Mo sites of the iron-molybdenum cofactor of nitrogenase with respect to binding and activation of N(2) have been studied by molecular mechanics calculations on the local protein environment and by density functional theory (DFT) calculations on subsections of the cofactor. The DFT calculat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi025623z

    authors: Durrant MC

    更新日期:2002-11-26 00:00:00

  • Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families.

    abstract::Database searches indicated that the genome of Bacillus subtilis contains three different genes encoding RNase H homologues. The ypdQ gene encodes an RNase HI homologue with 132 amino acid residues, whereas the rnh and ysgB genes encode RNase HII homologues with 255 and 313 amino acid residues, respectively. RNases HI...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi982207z

    authors: Ohtani N,Haruki M,Morikawa M,Crouch RJ,Itaya M,Kanaya S

    更新日期:1999-01-12 00:00:00

  • Spectral properties of environmentally sensitive probes associated with horseradish peroxidase.

    abstract::The environmentally sensitive fluorescent probes 6-propionyl-2-(N,N-dimethylamino)naphthalene (PRODAN) and 2'-(N,N-dimethylamino)-6-naphthoyl-4-trans-cyclohexanioc acid (DANCA) form complexes with the heme binding site of apohorseradish peroxidase. The dissociation constants of the PRODAN and DANCA complexes were dete...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi951983t

    authors: Lasagna M,Vargas V,Jameson DM,Brunet JE

    更新日期:1996-01-23 00:00:00

  • Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme.

    abstract::To determine the energetic and structural consequences of placing a charged group within the core of a protein, two "buried charge" mutants, Met 102----Lys (M102K) and Leu 133----Asp (L133D) were constructed in phage T4 lysozyme. Both proteins fold at neutral pH, although they are substantially less stable than wild t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00113a006

    authors: Dao-pin S,Anderson DE,Baase WA,Dahlquist FW,Matthews BW

    更新日期:1991-12-10 00:00:00

  • Autocatalytic acylation of phospholipase-like myotoxins.

    abstract::Several snake venoms contain a phospholipase A2 in which position 49 in the active site is occupied by a lysine or a serine instead of the aspartate residue normally found. Although these proteins do not bind Ca2+ and are devoid of catalytic activity, they are still highly specific myotoxins and have recently been sho...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00014a021

    authors: Pedersen JZ,Lomonte B,Massoud R,Gubensek F,Gutiérrez JM,Rufini S

    更新日期:1995-04-11 00:00:00

  • Analysis of neuronal NO synthase under single-turnover conditions: conversion of Nomega-hydroxyarginine to nitric oxide and citrulline.

    abstract::Nitric oxide synthases (NOSs) are proposed to generate NO and citrulline from L-arginine in two steps: initial N-hydroxylation to generate Nomega-hydroxyarginine (NOHA) followed by a three-electron oxidation of the hydroxylated nitrogen to form products. Both steps consume NADPH and may involve heme iron-based activat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971414g

    authors: Abu-Soud HM,Presta A,Mayer B,Stuehr DJ

    更新日期:1997-09-09 00:00:00

  • Progesterone-binding components of chick oviduct: analysis of receptor structure by limited proteolysis.

    abstract::An endogenous calcium-activated sulfhydryl protease in chick oviduct cytosol has been utilized to study the structure of the chick oviduct progesterone receptor subunits, progestophilins A (79 000 g/mol) and B (117 000 g/mol). The protease is not a normal component of the native progesterone receptor aggregate (6 and ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00543a015

    authors: Vedeckis WV,Schrader WT,O'Malley BW

    更新日期:1980-01-22 00:00:00

  • Probe of beta-galactosidase structure with iodoacetate. Differential reactivity of thiol groups in wild-type and mutant forms of beta-galactosidase.

    abstract::Carboxymethylation with 14 C-labeled iodoacetate of cysteine residues in wild-type beta-galactosidase from Escherichia coli and in a defective beta-galactosidase from deletion mutant strain M15 was investigated in order to determine accessible positions in the tetrameric wild-type form and the dimeric mutant M15 prote...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00617a015

    authors: Jörnvall H,Fowler AV,Zabin I

    更新日期:1978-11-28 00:00:00

  • Sequential domain unfolding in phosphoglycerate kinase: fluorescence intensity and anisotropy stopped-flow kinetics of several tryptophan mutants.

    abstract::Stopped-flow total intensity and anisotropy experiments on single tryptophan containing mutants of yeast phosphoglycerate kinase (PGK) located in either the carboxy-terminal domain (W308 and W333), amino-terminal domain (W48 and W122), or "hinge" region (W194 and W399) were performed. The results obtained for single t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00042a028

    authors: Beechem JM,Sherman MA,Mas MT

    更新日期:1995-10-24 00:00:00

  • Expression and sequence analyses of serum amyloid A in the Syrian hamster.

    abstract::Reactive amyloidosis occurs during chronic inflammation and involves deposition of amyloid A (AA) fibrils in many organs. Amyloid A is derived by proteolysis from serum amyloid A component (SAA), a major acute-phase reactant in many species. Since spontaneous amyloidosis occurs commonly in Syrian hamsters, we have stu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00437a040

    authors: Webb CF,Tucker PW,Dowton SB

    更新日期:1989-05-30 00:00:00

  • Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid).

    abstract::The Raman laser temperature-jump technique has been used to measure the kinetics of the coil to helix reaction of poly(cytidylic acid) [poly(C)] in aqueous cosolvent mixtures. The rate of helix formation has a low activation energy and is proportional to reciprocal solvent viscosity. The observations suggest helix for...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00509a003

    authors: Freier SM,Hill KO,Dewey TG,Marky LA,Breslauer KJ,Turner DH

    更新日期:1981-03-17 00:00:00

  • Penicillanic acid sulfone: an unexpected isotope effect in the interaction of 6 alpha- and 6 beta-monodeuterio and of 6,6-dideuterio derivatives with RTEM beta-lactamase from Escherichia coli.

    abstract::Penicillanic acid sulfone (1) is both a substrate and an inactivator of the RTEM beta-lactamase. About 7000 hydrolytic events occur before enzyme inactivation. The 6,6-dideuterio sulfone shows a 3-fold acceleration of both the hydrolysis reaction and the enzyme inactivation. The kinetic and spectroscopic results are n...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00516a003

    authors: Brenner DG,Knowles JR

    更新日期:1981-06-23 00:00:00

  • Structure of the S100A6 complex with a fragment from the C-terminal domain of Siah-1 interacting protein: a novel mode for S100 protein target recognition.

    abstract::S100A6 is a member of the S100 subfamily of EF-hand Ca (2+) binding proteins that has been shown to interact with calcyclin binding protein/Siah-1 interacting protein (CacyBP/SIP or SIP), a subunit of an SCF-like E3 ubiquitin ligase complex (SCF-TBL1) formed under genotoxic stress. SIP serves as a scaffold in this com...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801233z

    authors: Lee YT,Dimitrova YN,Schneider G,Ridenour WB,Bhattacharya S,Soss SE,Caprioli RM,Filipek A,Chazin WJ

    更新日期:2008-10-14 00:00:00

  • Heme binding properties of glyceraldehyde-3-phosphate dehydrogenase.

    abstract::Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that also functions in transcriptional regulation, oxidative stress, vesicular trafficking, and apoptosis. Because GAPDH is required for the insertion of cellular heme into inducible nitric oxide synthase [Chakravarti, R., et al. (2010) Proc. Natl...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi300863a

    authors: Hannibal L,Collins D,Brassard J,Chakravarti R,Vempati R,Dorlet P,Santolini J,Dawson JH,Stuehr DJ

    更新日期:2012-10-30 00:00:00