A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.

Abstract:

:The conformational properties of an active-site loop segment, defined by residues Ser(161)-Glu(162)-Asn(163)-Ser(164), have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen-bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity. Heavy-atom isotope effect measurements, in combination with the X-ray crystal structure of the T165V OxDC variant, demonstrate that the conserved Arg/Thr hydrogen bond is important for correctly locating the side chain of Glu-162, which mediates a proton-coupled electron transfer (PCET) step prior to decarboxylation in the catalytically competent form of OxDC. In addition, we show that the T165V OxDC variant exhibits a lower level of oxalate consumption per dioxygen molecule, consistent with the predictions of recent spin-trapping experiments [Imaram et al. (2011) Free Radicals Biol. Med. 50, 1009-1015]. This finding implies that dioxygen might participate as a reversible electron sink in two putative PCET steps and is not merely used to generate a protein-based radical or oxidized metal center.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Saylor BT,Reinhardt LA,Lu Z,Shukla MS,Nguyen L,Cleland WW,Angerhofer A,Allen KN,Richards NG

doi

10.1021/bi300001q

subject

Has Abstract

pub_date

2012-04-03 00:00:00

pages

2911-20

issue

13

eissn

0006-2960

issn

1520-4995

journal_volume

51

pub_type

杂志文章
  • Disparate molecular dynamics of plasmenylcholine and phosphatidylcholine bilayers.

    abstract::The molecular dynamics of binary dispersions of plasmenylcholine/cholesterol and phosphatidylcholine/cholesterol were quantified by electron spin resonance (ESR) and deuterium magnetic resonance (2H NMR) spectroscopy. The order parameter of both 5-doxylstearate (5DS) and 16-doxylstearate (16DS) was larger in vesicles ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00389a033

    authors: Pak JH,Bork VP,Norberg RE,Creer MH,Wolf RA,Gross RW

    更新日期:1987-07-28 00:00:00

  • Systematic comparison of statistical analyses of electronic and vibrational circular dichroism for secondary structure prediction of selected proteins.

    abstract::The electronic (ultraviolet) circular dichroism (UVCD) and vibrational circular dichroism (VCD) of 20 proteins are systematically compared as to their relationship to the secondary structures of these proteins. The UVCD spectra are statistically treated by use of the same factor analysis methods used previously for VC...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00242a012

    authors: Pancoska P,Keiderling TA

    更新日期:1991-07-16 00:00:00

  • Molecular modeling of the multidomain structures of the proteoglycan binding region and the link protein of cartilage by neutron and synchrotron X-ray scattering.

    abstract::The interaction of proteoglycan monomers with hyaluronate in cartilage is mediated by a globular binding region at the N-terminus of the proteoglycan monomer; this interaction is stabilized by link protein. Sequences show that both the binding region (27% carbohydrate) and the link protein (6% carbohydrate) contain an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00108a015

    authors: Perkins SJ,Nealis AS,Dunham DG,Hardingham TE,Muir IH

    更新日期:1991-11-05 00:00:00

  • Presence of two rhodopsin intermediates responsible for transducin activation.

    abstract::To identify how many rhodopsin intermediates interact with retinal G-protein transducin, the photobleaching process of chicken rhodopsin has been investigated in the presence or absence of transducin by means of time-resolved low-temperature spectroscopy. Singular value decomposition (SVD) analysis of the spectral dat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970932o

    authors: Tachibanaki S,Imai H,Mizukami T,Okada T,Imamoto Y,Matsuda T,Fukada Y,Terakita A,Shichida Y

    更新日期:1997-11-18 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

  • 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

  • Toward engineering the stability and hemin-binding properties of microsomal cytochromes b5 into rat outer mitochondrial membrane cytochrome b5: examining the influence of residues 25 and 71.

    abstract::As part of a larger effort to engineer the stability and hemin-binding properties of microsomal (Mc) cytochromes b(5) into rat liver outer mitochondrial membrane (OM) cytochrome (cyt) b(5), several mutants of rat OM cyt b(5) were prepared to study the effect of gradual and complete elimination of two extended hydropho...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi026005l

    authors: Cowley AB,Altuve A,Kuchment O,Terzyan S,Zhang X,Rivera M,Benson DR

    更新日期:2002-10-01 00:00:00

  • Dynamics of light-induced conformational changes of the phoborhodopsin/transducer complex formed in the n-dodecyl beta-D-maltoside micelle.

    abstract::A complex of photoreceptor phoborhodopsin (ppR; also called sensory rhodopsin II) and its cognate halobacterial transducer II (pHtrII) existing in the plasma membrane mediates the light signal to the cytoplasm in the earliest step of negative phototaxis in Natronomonas pharaonis. We have investigated the dynamics of t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi602482s

    authors: Taniguchi Y,Ikehara T,Kamo N,Yamasaki H,Toyoshima Y

    更新日期:2007-05-08 00:00:00

  • The multifunctional protein nucleophosmin (NPM1) is a human linker histone H1 chaperone.

    abstract::Linker histone H1 plays an essential role in chromatin organization. Proper deposition of linker histone H1 as well as its removal is essential for chromatin dynamics and function. Linker histone chaperones perform this important task during chromatin assembly and other DNA-templated phenomena in the cell. Our in vitr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi101835j

    authors: Gadad SS,Senapati P,Syed SH,Rajan RE,Shandilya J,Swaminathan V,Chatterjee S,Colombo E,Dimitrov S,Pelicci PG,Ranga U,Kundu TK

    更新日期:2011-04-12 00:00:00

  • Ribosome subunit to polysome ratios affect the synthesis of rRNA in Drosophila cells.

    abstract::Many investigations have revealed that ribosome numbers increase in parallel with the growth rate of cells. Here we show that the absolute level of protein synthesis may not be the only factor influencing rRNA synthesis in a nondividing eukaryotic cell. Under conditions of complete (greater than 99%) inhibition of pro...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00502a003

    authors: Yamamoto KK,Pellegrini M

    更新日期:1990-12-18 00:00:00

  • Complete amino acid sequence of the 4Fe-4S, thermostable ferredoxin from Clostridium thermoaceticum.

    abstract::The complete amino acid sequence of the 4Fe-4S ferredoxin from the thermophilic bacterium Clostridium thermoaceticum has been determined. The protein is extremely thermostable and is the only known clostridial ferredoxin to contain a single [4Fe-4S] cluster. The sequence totals 63 residues and includes the first trypt...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00257a007

    authors: Elliott JI,Yang SS,Ljungdahl LG,Travis J,Reilly CF

    更新日期:1982-07-06 00:00:00

  • The amino acid sequence of chick skin collagen alpha1-CB7.

    abstract::The amino acid sequence of chick skin collagen alpha1-CB7, the 268 CNBr peptide from the helical portion of the alpha1 chain, has been determined by automatic and manual degradation of tryptic and chymotryptic peptides, and of the COOH-terminal fragment produced by cleavage with animal collagenase. The resulting seque...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00684a013

    authors: Highberger JH,Corbett C,Kang AH,Gross J

    更新日期:1975-07-01 00:00:00

  • Glycosylation of recombinant prorenin in insect cells: the insect cell line Sf9 does not express the mannose 6-phosphate recognition signal.

    abstract::Sf9 cells infected with a recombinant baculovirus containing the gene for human prorenin were cultured in the presence of [3H]mannose. In vivo labeled prorenin was isolated by immunoprecipitation from the culture medium and digested with Pronase. The oligosaccharide structures on the resulting glycopeptides were analy...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00195a022

    authors: Aeed PA,Elhammer AP

    更新日期:1994-07-26 00:00:00

  • n-Alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and siderophore biosynthetic enzyme PvdQ.

    abstract::The enzyme PvdQ (E.C. 3.5.1.97) from Pseudomonas aeruginosa is an N-terminal nucleophile hydrolase that catalyzes the removal of an N-myristyl substituent from a biosynthetic precursor of the iron-chelating siderophore pyoverdine. Inhibitors of pyoverdine biosynthesis are potential antibiotics since iron is essential ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi501086s

    authors: Clevenger KD,Wu R,Liu D,Fast W

    更新日期:2014-10-28 00:00:00

  • Alteration of conformation and dynamics of bacteriorhodopsin induced by protonation of Asp 85 and deprotonation of Schiff base as studied by 13C NMR.

    abstract::According to previous X-ray diffraction studies, the D85N mutant of bacteriorhodopsin (bR) with unprotonated Schiff base assumes a protein conformation similar to that in the M photointermediate. We recorded (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled D85N and D85N/D96N mutants at ambient temperature t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0015820

    authors: Kawase Y,Tanio M,Kira A,Yamaguchi S,Tuzi S,Naito A,Kataoka M,Lanyi JK,Needleman R,Saitô H

    更新日期:2000-11-28 00:00:00

  • Reconstitution of bovine procarboxypeptidase A-S6 from the free subunits.

    abstract::The three subunits I, II, and III of bovine procarboxypeptidase A separated by reversible dimethylmaleylation can reassociate to form the reconstituted complexes I + II, I + III, and I + II + III. Since the association II + III is not possible, subunit I appears to play a central role in the formation of the complex. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00630a028

    authors: Puigserver A,Desnuelle P

    更新日期:1977-05-31 00:00:00

  • Structural consequences of cysteinylation of Cu/Zn-superoxide dismutase.

    abstract::The metalloenzyme Cu/Zn-superoxide dismutase (SOD1) catalyzes the reduction of superoxide anions into molecular oxygen and hydrogen peroxide. Hydrogen peroxide can oxidize SOD1, resulting in aberrant protein conformational changes, disruption of SOD1 function, and DNA damage. Cells may have evolved mechanisms of regul...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi400613h

    authors: Auclair JR,Brodkin HR,D'Aquino JA,Petsko GA,Ringe D,Agar JN

    更新日期:2013-09-10 00:00:00

  • Manganese-binding proteins of the oxygen-evolving complex.

    abstract::The extrinsic 33-kDa protein (P33) was cross-linked covalently to the binding site on P33-depleted PSII preparations which is responsible for reconstitution of photosynthetic water oxidation after PSII preparations have been washed with 1 M CaCl2. Conditions were found in which more than half of the cross-linked prote...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00439a033

    authors: Mei R,Green JP,Sayre RT,Frasch WD

    更新日期:1989-06-27 00:00:00

  • Dynamics of activation of lecithin:cholesterol acyltransferase by apolipoprotein A-I.

    abstract::The product of transesterification of phospholipid acyl chains and unesterified cholesterol (UC) by the enzyme lecithin:cholesterol acyltransferase (LCAT) is cholesteryl ester (CE). Activation of LCAT by apolipoprotein (apo) A-I on nascent (discoidal) high-density lipoproteins (HDL) is essential for formation of matur...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi901242k

    authors: Jones MK,Catte A,Li L,Segrest JP

    更新日期:2009-12-01 00:00:00

  • Comparison of the crystal and solution structures of calmodulin and troponin C.

    abstract::X-ray solution scattering data from skeletal muscle troponin C and from calmodulin have been measured. Modeling studies based on the crystal structure coordinates for these proteins show discrepancies between the solution data and the crystal structure that indicate that if the size and shape of the globular domains a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00403a011

    authors: Heidorn DB,Trewhella J

    更新日期:1988-02-09 00:00:00

  • Chemical modification of tryptophan residues in Escherichia coli succinyl-CoA synthetase. Effect on structure and enzyme activity.

    abstract::Succinyl-CoA synthetase of Escherichia coli is an alpha 2 beta 2 protein containing active sites at the interfaces between alpha- and beta-subunits. The alpha-subunit contains a histidine residue that is phosphorylated during the reaction. The beta-subunit binds coenzyme A and probably succinate [see Nishimura, J. S. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00370a061

    authors: Ybarra J,Prasad AR,Nishimura JS

    更新日期:1986-11-04 00:00:00

  • Modular mutagenesis of exons 1, 2, and 8 of a glutathione S-transferase from the mu class. Mechanistic and structural consequences for chimeras of isoenzyme 3-3.

    abstract::Exons 1 and 2 and exon 8 of the mu class GSH transferases from rat encode sequence-variable regions 1 and 4 of mu class isoenzymes, respectively. These two of four variable regions are located at the N- and C-termini of this isoenzyme class and impinge on the active site. In order to assess the influence of these vari...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00157a005

    authors: Zhang P,Liu S,Shan SO,Ji X,Gilliland GL,Armstrong RN

    更新日期:1992-10-27 00:00:00

  • Interactions between phospholipids and NADH:ubiquinone oxidoreductase (complex I) from bovine mitochondria.

    abstract::NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria is a highly complicated, energy transducing, membrane-bound enzyme. It contains 46 different subunits and nine redox cofactors: a noncovalently bound flavin mononucleotide and eight iron-sulfur clusters. The mechanism of complex I is not known. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051809x

    authors: Sharpley MS,Shannon RJ,Draghi F,Hirst J

    更新日期:2006-01-10 00:00:00

  • Heterologous expression of photoreceptor peripherin/rds and Rom-1 in COS-1 cells: assembly, interactions, and localization of multisubunit complexes.

    abstract::Peripherin/rds is a 39 kDa integral membrane glycoprotein essential for normal photoreceptor cell development in vertebrates. It has been implicated in several human retinal degenerative diseases including retinitis pigmentosa and macular degeneration and is thought to play a structural role at photoreceptor outer seg...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00043a028

    authors: Goldberg AF,Moritz OL,Molday RS

    更新日期:1995-10-31 00:00:00

  • Nanosecond fluorescence studies of noncovalent interaction of monomeric and dimeric intercalators with DNA.

    abstract::The noncovalent interaction of 2-aminodipyrido[1,2-a:3',2'-d]imidazole (Glu-P-2) and its derivatives, which are potent mutagens isolated from L-glutamic acid pyrolysate, with calf thymus DNA was studied by steady-state and nanosecond fluorescence spectroscopies. The fluorescence of these compounds exhibits static quen...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00344a013

    authors: Itoh M,Kurokawa H,Usui M,Ohno M,Shimoda E,Hashimoto Y,Shudo K

    更新日期:1985-11-05 00:00:00

  • Isolation and characterization of independently folding regions of the beta chain of Escherichia coli tryptophan synthetase.

    abstract::It had been reported previously that the beta2 subunit of Escherichia coli tryptophan synthetase [L-serinehydrolyase (adding indole) EC 4.2.1.20] can be cleaved by trypsin into a nearly functional dimeric protein, the monomer of which consists of two large, nonoverlapping, polypeptide fragments. In the present paper, ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00637a012

    authors: Högberg-Raibaud A,Goldberg ME

    更新日期:1977-09-06 00:00:00

  • An amino acid residue (S201) in the retinal binding pocket regulates the photoreaction pathway of phoborhodopsin.

    abstract::Phoborhodopsin from Halobacterium salinarum (salinarum phoborhodopsin, spR also called HsSR II) is a photoreceptor for the negative phototaxis of the bacterium. A unique feature of spR is the formation of a shorter wavelength photoproduct, P480, observed at liquid nitrogen temperature beside the K intermediate. Format...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200598r

    authors: Dai G,Zhang Y,Tamogami J,Demura M,Kamo N,Kandori H,Iwasa T

    更新日期:2011-08-23 00:00:00

  • ABC transporters and immunity: mechanism of self-defense.

    abstract::The transporter associated with antigen processing (TAP) is a prototype of an asymmetric ATP-binding cassette (ABC) transporter, which uses ATP binding and hydrolysis to translocate peptides from the cytosol to the lumen of the endoplasmic reticulum (ER). Here, we review molecular details of peptide binding and ATP bi...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/bi300128f

    authors: Hinz A,Tampé R

    更新日期:2012-06-26 00:00:00

  • Tertiary structure stability of the hairpin ribozyme in its natural and minimal forms: different energetic contributions from a ribose zipper motif.

    abstract::The hairpin catalytic motif in tobacco ringspot virus satellite RNA consists of two helix-loop-helix elements on two adjacent arms of a four-way helical junction. The bases essential for catalytic activity are located in the loops that are brought into proximity by a conformational change as a prerequisite for catalys...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010773f

    authors: Klostermeier D,Millar DP

    更新日期:2001-09-18 00:00:00

  • The Structure of the Bimolecular Complex between Amphotericin B and Ergosterol in Membranes Is Stabilized by Face-to-Face van der Waals Interaction with Their Rigid Cyclic Cores.

    abstract::Amphotericin B (AmB) is a polyene macrolide antibiotic isolated from Streptomyces nodosus. The antifungal activity of AmB can be attributed to the formation of an ion-channel assembly in the presence of ergosterol (Erg), in which there are two different AmB-Erg orientations, parallel and antiparallel, as reported prev...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00193

    authors: Nakagawa Y,Umegawa Y,Matsushita N,Yamamoto T,Tsuchikawa H,Hanashima S,Oishi T,Matsumori N,Murata M

    更新日期:2016-06-21 00:00:00