A conformational mimic of the MgATP-bound "on state" of the nitrogenase iron protein.

Abstract:

:The crystal structure of a nitrogenase Fe protein single site deletion variant reveals a distinctly new conformation of the Fe protein and indicates that, upon binding of MgATP, the Fe protein undergoes a dramatic conformational change that is largely manifested in the rigid-body reorientation of the homodimeric Fe protein subunits with respect to one another. The observed conformational state allows the rationalization of a model of structurally and chemically complementary interactions that occur upon initial complex formation with the MoFe protein component that are distinct from the protein-protein interactions that have been characterized previously for stabilized nitrogenase complexes. The crystallographic results, in combination with complementary UV-visible absorption, EPR, and resonance Raman spectroscopic data, indicate that the [4Fe-4S] cluster of both the Fe protein deletion variant and the native Fe protein in the presence of MgATP can reversibly cycle between a regular cubane-type [4Fe-4S] cluster in the reduced state and a cleaved form involving two [2Fe-2S] fragments in the oxidized state. Resonance Raman studies indicate that this novel cluster conversion is induced by glycerol, and the crystallographic data suggest that glycerol is bound as a bridging bidentate ligand to both [2Fe-2S] cluster fragments in the oxidized state.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Sen S,Igarashi R,Smith A,Johnson MK,Seefeldt LC,Peters JW

doi

10.1021/bi0358465

subject

Has Abstract

pub_date

2004-02-24 00:00:00

pages

1787-97

issue

7

eissn

0006-2960

issn

1520-4995

journal_volume

43

pub_type

杂志文章
  • Quantitative characterization of the binding of plasminogen to intact fibrin clots, lysine-sepharose, and fibrin cleaved by plasmin.

    abstract::The binding of human Glu- and Lys-plasminogens to intact fibrin clots, to lysine-Sepharose, and to fibrin cleaved by plasmin was quantitatively characterized. On intact fibrin clots, there was one strong binding site for Glu-plasminogen with a dissociation constant, Kd, of 25 microM and one strong binding site for Lys...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00334a031

    authors: Bok RA,Mangel WF

    更新日期:1985-06-18 00:00:00

  • Importance of two buried salt bridges in the stability and folding pathway of barnase.

    abstract::The importance of two buried salt bridges in barnase in the stability of its folded state, the major transition rate for unfolding, and a folding intermediate has been analyzed by protein engineering, kinetic, and thermodynamic studies. The aspartate residues in the bridges Arg69-Asp93 and Arg83-Asp75 were replaced by...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi952930e

    authors: Tissot AC,Vuilleumier S,Fersht AR

    更新日期:1996-05-28 00:00:00

  • Fluorescent probes as a measure of conformational alterations induced by nucleophilic modification and proteolysis of bovine alpha 2-macroglobulin.

    abstract::Conformational alterations occurring in bovine alpha 2-macroglobulin (alpha 2M) resulting from proteolysis and nucleophilic modification have been monitored by UV difference spectra, circular dichroism, and changes in the fluorescence of 6-(p-toluidino)-2-naphthalenesulfonate (TNS) and bis(8-anilino-1-naphthalenesulfo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00321a061

    authors: Strickland DK,Steiner JP,Feldman SR,Pizzo SV

    更新日期:1984-12-18 00:00:00

  • Mechanism of protein salting in and salting out by divalent cation salts: balance between hydration and salt binding.

    abstract::The preferential interactions of proteins with solvent components were studied in concentrated aqueous solutions of the sulfate, acetate, and chloride salts of Mg2+, Ba2+, Ca2+, Mn2+ and Ni2+ [except for CaSO4, BaSO4, Mn-(OAc)2, and Ni(OAc)2], and results were compared with those of the Na+ salts. It was found that, f...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00320a004

    authors: Arakawa T,Timasheff SN

    更新日期:1984-12-04 00:00:00

  • Polymer models of protein stability, folding, and interactions.

    abstract::The unfolded state and flexible linkers in the folded structure play essential roles in protein stability and folding and protein-protein interactions. Intrinsic to these roles is the fact that unfolded proteins and flexible linkers sample many different conformations. Polymer models may capture this and complement ex...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi036269n

    authors: Zhou HX

    更新日期:2004-03-02 00:00:00

  • Conformation and dynamics of the Pribnow box region of the self-complementary d(C-G-A-T-T-A-T-A-A-T-C-G) duplex in solution.

    abstract::Nuclear magnetic resonance (NMR) has been used to monitor the conformation and dynamics of the d(C1-G2-A3-T4-T5-A6-T6-A5-A4-T3-C2-G1) self-complementary dodecanucleotide duplex (henceforth called Pribnow 12-mer), which contains a TATAAT Pribnow box and a central core of eight dA X dT base pairs. The exchangeable imino...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00325a019

    authors: Patel DJ,Kozlowski SA,Weiss M,Bhatt R

    更新日期:1985-02-12 00:00:00

  • Kinetics of ribosome dissociation and subunit association studied in a light-scattering stopped-flow apparatus.

    abstract::The association-dissociation kinetics of ribosomes from Escherichia coli have been studied under various conditions in a light-scattering stopped-flow apparatus. The dissociation reaction at 2 mg/ml at 25 degrees C, induced by lowering the MgCl2 concentration from 18 to 3 mM, can best be described by three independent...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00671a010

    authors: Görisch H,Goss DJ,Parkhurst LJ

    更新日期:1976-12-28 00:00:00

  • Coordinating role of His216 in MgATP binding and cleavage in pyruvate carboxylase.

    abstract::His216 is a well-conserved residue in pyruvate carboxylases and, on the basis of structures of the enzyme, appears to have a role in the binding of MgATP, forming an interaction with the 3'-hydroxyl group of the ribose ring. Mutation of this residue to asparagine results in a 9-fold increase in the Km for MgATP in its...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi4016814

    authors: Adina-Zada A,Jitrapakdee S,Wallace JC,Attwood PV

    更新日期:2014-02-18 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

  • Mutagenesis of subunit N of the Escherichia coli complex I. Identification of the initiation codon and the sensitivity of mutants to decylubiquinone.

    abstract::The last gene in the nuo operon of Escherichia coli, nuoN, encodes a membrane-bound subunit of Complex I (NADH:ubiquinone oxidoreductase). In this report, the gene for subunit N was disrupted by a 163 bp deletion in the chromosome, resulting in the loss of Complex I function, as measured by deamino-NADH oxidase activi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0340346

    authors: Amarneh B,Vik SB

    更新日期:2003-05-06 00:00:00

  • Location of an alpha-helix in fragment 96-133 from bovine somatotropin by 1H NMR spectroscopy.

    abstract::By use of two-dimensional NMR techniques most of the proton resonances (greater than 90%) are assigned for the tryptic digest fragment 96-133 of bovine somatotropin in 30% 2,2,2-trifluoroethanol-d3/70% H2O. Qualitative analysis of the nuclear Overhauser enhancement (NOE) data indicates that a region of alpha-helix spa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00411a020

    authors: Gooley PR,MacKenzie NE

    更新日期:1988-05-31 00:00:00

  • Regulation of actin filament dynamics by actin depolymerizing factor/cofilin and actin-interacting protein 1: new blades for twisted filaments.

    abstract::Actin depolymerizing factor (ADF)/cofilin enhances turnover of actin filaments by severing and depolymerizing filaments. A number of proteins functionally interact with ADF/cofilin to modulate the dynamics of actin filaments. Actin-interacting protein 1 (AIP1) has emerged as a conserved WD-repeat protein that specific...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/bi034600x

    authors: Ono S

    更新日期:2003-11-25 00:00:00

  • Secondary structure in properdin of the complement cascade and related proteins: a study by Fourier transform infrared spectroscopy.

    abstract::Six structural repeat motifs of 58 amino acids are found in the sequence of both mouse and human properdins. Twelve more examples of the motif are available from the sequences of thrombospondin, the terminal complement components, and the thrombospondin-related anonymous protein. The averaged Robson and Chou-Fasman se...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00444a007

    authors: Perkins SJ,Nealis AS,Haris PI,Chapman D,Goundis D,Reid KB

    更新日期:1989-09-05 00:00:00

  • Subgel phases of n-saturated diacylphosphatidylcholines: a Fourier-transform infrared spectroscopic study.

    abstract::The subgel phases of a homologous series of saturated straight-chain diacylphosphatidylcholines with hydrocarbon chains consisting of 10-18 carbon atoms were studied by Fourier-transform infrared spectroscopy. All of these lipids initially form a subgel phase which is spectroscopically similar to that obtained when fu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00486a024

    authors: Lewis RN,McElhaney RN

    更新日期:1990-08-28 00:00:00

  • Targeting of protein phosphatases PP2A and PP2B to the C-terminus of the L-type calcium channel Ca v1.2.

    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

    authors: Xu H,Ginsburg KS,Hall DD,Zimmermann M,Stein IS,Zhang M,Tandan S,Hill JA,Horne MC,Bers D,Hell JW

    更新日期:2010-12-07 00:00:00

  • Elucidation of the functional metal binding profile of a Cd(II)/Pb(II) sensor CmtR(Sc) from Streptomyces coelicolor.

    abstract::Metal homeostasis and resistance in bacteria is maintained by a panel of metal-sensing transcriptional regulators that collectively control transition metal availability and mediate resistance to heavy metal xenobiotics, including As(III), Cd(II), Pb(II), and Hg(II). The ArsR family constitutes a superfamily of metal ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi100490u

    authors: Wang Y,Kendall J,Cavet JS,Giedroc DP

    更新日期:2010-08-10 00:00:00

  • Recombinant human CNTF receptor alpha: production, binding stoichiometry, and characterization of its activity as a diffusible factor.

    abstract::The primary ligand-binding protein (CNTFR alpha) of the multicomponent receptor for ciliary neurotrophic factor was produced in Escherichia coli. Using novel applications of size-exclusion chromatography and a protein gel-shift assay, we obtained quantitative separation of correctly refolded protein, as well as analyt...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00185a020

    authors: Panayotatos N,Everdeen D,Liten A,Somogyi R,Acheson A

    更新日期:1994-05-17 00:00:00

  • Heightened Dynamics of the Oxidized Y48H Variant of Human Cytochrome c Increases Its Peroxidatic Activity.

    abstract::Proteins performing multiple biochemical functions are called "moonlighting proteins" or extreme multifunctional (EMF) proteins. Mitochondrial cytochrome c is an EMF protein that binds multiple partner proteins to act as a signaling molecule, transfers electrons in the respiratory chain, and acts as a peroxidase in ap...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00890

    authors: Deacon OM,Karsisiotis AI,Moreno-Chicano T,Hough MA,Macdonald C,Blumenschein TMA,Wilson MT,Moore GR,Worrall JAR

    更新日期:2017-11-21 00:00:00

  • Functional segregation of a predicted "hinge" site within the beta-strand linkers of Escherichia coli leucyl-tRNA synthetase.

    abstract::Some aminoacyl-tRNA synthetases (AARSs) employ an editing mechanism to ensure the fidelity of protein synthesis. Leucyl-tRNA synthetase (LeuRS), isoleucyl-tRNA synthetase (IleRS), and valyl-tRNA synthetase (ValRS) share a common insertion, called the CP1 domain, which is responsible for clearing misformed products. Th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi702494q

    authors: Mascarenhas AP,Martinis SA

    更新日期:2008-04-22 00:00:00

  • The SIV tilted peptide induces cylindrical reverse micelles in supported lipid bilayers.

    abstract::Elucidation of the molecular mechanism leading to biomembrane fusion is a challenging issue in current biomedical research in view of its involvement in controlling cellular functions and in mediating various important diseases. According to the generally admitted stalk mechanism described for membrane fusion, negativ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi060317x

    authors: El Kirat K,Dufrêne YF,Lins L,Brasseur R

    更新日期:2006-08-01 00:00:00

  • Equilibrium analysis of ethidium binding to DNA containing base mismatches and branches.

    abstract::In the processes of DNA replication, recombination, and repair, duplex DNA can transiently form branched structures, such as Holliday junctions, as well as base pair mismatches and bulges. These stages have altered ligand and protein binding properties from normal double helical DNA. A variety of ligands have been rep...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00248a025

    authors: Hernández LI,Zhong M,Courtney SH,Marky LA,Kallenbach NR

    更新日期:1994-11-08 00:00:00

  • Structural Insight into the Discrimination between 8-Oxoguanine Glycosidic Conformers by DNA Repair Enzymes: A Molecular Dynamics Study of Human Oxoguanine Glycosylase 1 and Formamidopyrimidine-DNA Glycosylase.

    abstract::hOgg1 and FPG are the primary DNA repair enzymes responsible for removing the major guanine (G) oxidative product, namely, 7,8-dihydro-8-oxoguanine (OG), in humans and bacteria, respectively. While natural G adopts the anti conformation and forms a Watson-Crick pair with cytosine (C), OG can also adopt the syn conform...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b01292

    authors: Sowlati-Hashjin S,Wetmore SD

    更新日期:2018-02-20 00:00:00

  • Slow refolding kinetics in yeast iso-2 cytochrome c.

    abstract::In refolding of iso-2 cytochrome c from Saccharomyces cerevisiae, there are two slow folding reactions, tau 1a and tau 1b. The slower of the slow reactions, tau 1a = 100-200 s, is observed only by absorbance changes, while tau 1b (10-20-fold faster) is detected by fluorescence changes. The temperature dependence of th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00348a024

    authors: Osterhout JJ Jr,Nall BT

    更新日期:1985-12-31 00:00:00

  • Structural Changes of the Active Center during the Photoactivation of Xenopus (6-4) Photolyase.

    abstract::Photolyases (PHRs) repair the UV-induced photoproducts, cyclobutane pyrimidine dimer (CPD) or pyrimidine-pyrimidone (6-4) photoproduct [(6-4) PP], restoring normal bases to maintain genetic integrity. CPD and (6-4) PP are repaired by substrate-specific PHRs, CPD PHR and (6-4) PHR, respectively. Flavin adenine dinucleo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b01111

    authors: Yamada D,Yamamoto J,Zhang Y,Iwata T,Hitomi K,Getzoff ED,Iwai S,Kandori H

    更新日期:2016-02-02 00:00:00

  • Copurification of the FpvA ferric pyoverdin receptor of Pseudomonas aeruginosa with its iron-free ligand: implications for siderophore-mediated iron transport.

    abstract::The Pseudomonas aeruginosa FpvA receptor is a TonB-dependent outer membrane transport protein that catalyzes uptake of ferric pyoverdin across the outer membrane. Surprisingly, FpvA expressed in P. aeruginosa grown in an iron-deficient medium copurifies with a ligand X that we have characterized by UV, fluorescence, a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi990421x

    authors: Schalk IJ,Kyslik P,Prome D,van Dorsselaer A,Poole K,Abdallah MA,Pattus F

    更新日期:1999-07-20 00:00:00

  • Recombinant hemoglobin(alpha 29leucine --> phenylalanine, alpha 96valine --> tryptophan, beta 108asparagine --> lysine) exhibits low oxygen affinity and high cooperativity combined with resistance to autoxidation.

    abstract::Using our hemoglobin expression system in Escherichia coli, we have constructed three recombinant hemoglobins (rHbs) with amino acid substitutions located in the alpha(1)beta(1) and alpha(1)beta(2) subunit interfaces and in the distal heme pocket of the alpha-chain: rHb(alphaV96W, betaN108K), rHb(alphaL29F, alphaV96W,...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991271t

    authors: Jeong ST,Ho NT,Hendrich MP,Ho C

    更新日期:1999-10-05 00:00:00

  • Librational motion of an "immobilized" spin label: hemoglobin spin labeled by a maleimide derivative.

    abstract::The spin label Tempo-maleimide, when "immobilized" in hemoglobin, is shown to exhibit motional fluctuation whose amplitude and/or frequency depend on temperature and solution conditions. These motional fluctuations are observable by several electron spin resonance techniques. For desalted hemoglobin the fluctuations a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00600a014

    authors: Johnson ME

    更新日期:1978-04-04 00:00:00

  • Integrin-supported fast rate intracellular delivery of plasmid DNA by extracellular matrix protein embedded calcium phosphate complexes.

    abstract::Extracellular matrix (ECM) proteins, such as collagen and fibronectin, play vital roles in development and maintenance of hard tissue (bone or tooth) and are, consequently, thoroughly investigated for construction of biomimetic scaffolds in combination with calcium phosphate (CaP) material (the major component of hard...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi050595g

    authors: Chowdhury EH,Nagaoka M,Ogiwara K,Zohra FT,Kutsuzawa K,Tada S,Kitamura C,Akaike T

    更新日期:2005-09-20 00:00:00

  • New clevable photoreactive heterobifunctional cross-linking reagents for studying membrane organization.

    abstract::The synthesis is described of four new cleavable, photosensitive, heterobifunctional cross-linking reagents for use in examining membrane organization: 4'-azidoazobenzene-4oxysuccinimide ester (1), N-[4-(p-azidophenylazo)benzoyl]-3-aminopropyl-N'-oxysuccinimide ester (2), N-[4-(p-azidophenylazo)benzoyl]-6-aminohexyl-N...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00560a007

    authors: Jaffe CL,Lis H,Sharon N

    更新日期:1980-09-16 00:00:00

  • Crystallographic studies of isosteric NAD analogues bound to alcohol dehydrogenase: specificity and substrate binding in two ternary complexes.

    abstract::CNAD (5-beta-D-ribofuranosylnicotinamide adenine dinucleotide) is an isosteric C-glycosidic analogue of NAD(H) containing a neutral pyridine ring. CPAD (5-beta-D-ribofuranosylpicolinamide adenine dinucleotide) is a closely related pyridine-containing analogue with the pyridine nitrogen on the opposite side of the ring...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00205a009

    authors: Li H,Hallows WH,Punzi JS,Pankiewicz KW,Watanabe KA,Goldstein BM

    更新日期:1994-10-04 00:00:00