1.9-A structures of ternary complexes of citrate synthase with D- and L-malate: mechanistic implications.

Abstract:

:The structures of four isomorphous crystals of ternary complexes of chicken heart citrate synthase with D- or L-malate and acetyl coenzyme A or carboxymethyl coenzyme A have been determined by X-ray crystallography and fully refined at 1.9-A resolution. The structures show that both L-malate and D-malate bind in a very similar way in the presence of acetylCoA and that the enzyme conformation is "closed". Hydrogen bond geometry is suggested to account for the difference in binding constants of the two stereoisomers. The structures suggest that steric hindrance can account for the observation that proton exchange of acetyl coenzyme A with solvent is catalyzed by citrate synthase in the presence of L-malate but not D-malate. The ternary complexes with malate reveal the mode of binding of the substrate acetylCoA in the ground state. The carbonyl oxygen of the acetyl group is hydrogen bonded to a water molecule and to histidine 274, allowing unambiguous identification of the orientation of this group. The structures support the hypothesis that carboxymethyl coenzyme A is a transition-state analogue for the enolization step of the reaction (Bayer et al., 1981) and additionally support proposed mechanisms for the condensation reaction (Karpusas et al., 1990; Alter et al., 1990).

journal_name

Biochemistry

journal_title

Biochemistry

authors

Karpusas M,Holland D,Remington SJ

doi

10.1021/bi00238a028

subject

Has Abstract

pub_date

1991-06-18 00:00:00

pages

6024-31

issue

24

eissn

0006-2960

issn

1520-4995

journal_volume

30

pub_type

杂志文章
  • Comparative electron paramagnetic resonance study of radical intermediates in turnip peroxidase isozymes.

    abstract::The occurrence of isozymes in plant peroxidases is poorly understood. Turnip roots contain seven season-dependent isoperoxidases with distinct physicochemical properties. In the work presented here, multifrequency electron paramagnetic resonance spectroscopy has been used to characterize the Compound I intermediate ob...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi002826j

    authors: Ivancich A,Mazza G,Desbois A

    更新日期:2001-06-12 00:00:00

  • Complete amino acid sequence of human liver cytosolic alanine aminotransferase (GPT) determined by a combination of conventional and mass spectral methods.

    abstract::The complete amino acid sequence of human liver cytosolic alanine aminotransferase (GPT) (EC 2.6.1.2) is presented. Two primary sets of overlapping fragments were obtained by cleavage of the pyridylethylated protein at methionyl and lysyl bonds with cyanogen bromide and Achromobacter protease I, respectively. Isolated...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00107a013

    authors: Ishiguro M,Takio K,Suzuki M,Oyama R,Matsuzawa T,Titani K

    更新日期:1991-10-29 00:00:00

  • Probing the Vibrio harveyi luciferase beta subunit functionality and the intersubunit domain by site-directed mutagenesis.

    abstract::While the critical role of the bacterial luciferase alpha subunit in catalysis has been amply documented, the beta subunit was only known to be involved in thermal stability and substrate binding. Two conserved histidyl residues at position 81 and 82 of the beta subunit of Vibrio harveyi luciferase were each mutated t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00206a023

    authors: Xin X,Xi L,Tu SC

    更新日期:1994-10-11 00:00:00

  • Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase.

    abstract::Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides and 2'-deoxyribonucleosides, yielding the purine base and (2'-deoxy)ribose 1-phosphate as products. While this enzyme has been extensively studied, several questions with respect to the catalytic mechanism have rema...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b01347

    authors: Isaksen GV,Hopmann KH,Åqvist J,Brandsdal BO

    更新日期:2016-04-12 00:00:00

  • Interaction of hemoglobin and its component alpha and beta chains with band 3 protein.

    abstract::The equilibrium binding of hemoglobin to isolated band 3 protein exhibited positive cooperativity [Hill coefficient = 1.65 +/- 0.1; total number of binding sites at pH 6.6 in 5 mM sodium phosphate buffer = 32 500 +/- 940 pmol/mg; Ka = (3.0 +/- 0.5) X 10(5) M-1]. The binding was reversible and ionic in nature as the bo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00359a054

    authors: Premachandra BR

    更新日期:1986-06-03 00:00:00

  • Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.

    abstract::Helix-junction-helix (HJH) motifs are flexible building blocks of RNA architecture that help define the orientation and dynamics of helical domains. They are also frequently involved in adaptive recognition of proteins and small molecules and in the formation of tertiary contacts. Here, we use a battery of nuclear mag...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00285

    authors: Merriman DK,Xue Y,Yang S,Kimsey IJ,Shakya A,Clay M,Al-Hashimi HM

    更新日期:2016-08-16 00:00:00

  • Argonaute Facilitates the Lateral Diffusion of the Guide along Its Target and Prevents the Guide from Being Pushed Away by the Ribosome.

    abstract::Argonaute (AGO) proteins play central roles in nucleic acid-guided interference that regulates gene expression and defend against foreign genetic elements in all life. Although much progress has been made with respect to the function of argonaute proteins in target recognition and cleavage, the detailed mechanism of t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b00213

    authors: Song G,Chen H,Sheng G,Wang Y,Lou J

    更新日期:2018-04-17 00:00:00

  • Conversion of aminodeoxychorismate synthase into anthranilate synthase with Janus mutations: mechanism of pyruvate elimination catalyzed by chorismate enzymes.

    abstract::The central importance of chorismate enzymes in bacteria, fungi, parasites, and plants combined with their absence in mammals makes them attractive targets for antimicrobials and herbicides. Two of these enzymes, anthranilate synthase (AS) and aminodeoxychorismate synthase (ADCS), are structurally and mechanistically ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00013

    authors: Culbertson JE,Chung Dh,Ziebart KT,Espiritu E,Toney MD

    更新日期:2015-04-14 00:00:00

  • Levuglandin forms adducts with histone h4 in a cyclooxygenase-2-dependent manner, altering its interaction with DNA.

    abstract::Inflammation and subsequent cyclooxygenase-2 (COX-2) activity has long been linked with the development of cancer, although little is known about any epigenetic effects of COX-2. A product of COX-2 activation, levuglandin (LG) quickly forms covalent bonds with nearby primary amines, such as those in lysine, which lead...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi401673b

    authors: Carrier EJ,Zagol-Ikapitte I,Amarnath V,Boutaud O,Oates JA

    更新日期:2014-04-22 00:00:00

  • Thioltransferase in human red blood cells: purification and properties.

    abstract::Thioltransferase activity was identified and the enzyme purified to apparent homogeneity from human red blood cells. Activity was measured as glutathione-dependent reduction of the prototype substrate hydroxyethyl disulfide; formation of oxidized glutathione (GSSG) was coupled to NADPH oxidation by GSSG reductase (1 u...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00239a002

    authors: Mieyal JJ,Starke DW,Gravina SA,Dothey C,Chung JS

    更新日期:1991-06-25 00:00:00

  • Organization of the human protein S genes.

    abstract::Human genomic clones that span the entire protein S expressed gene (PS alpha) and the 3' two-thirds of the protein S pseudogene (PS beta) have been isolated and characterized. The PS alpha gene is greater than 80 kilobases in length and contains 14 introns and 15 exons, as well as 6 repetitive "Alu" sequences. Exons I...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00486a010

    authors: Schmidel DK,Tatro AV,Phelps LG,Tomczak JA,Long GL

    更新日期:1990-08-28 00:00:00

  • Maintenance of alpha-helical structures by phenyl rings in the active-site tyrosine triad contributes to catalysis and stability of ketosteroid isomerase from Pseudomonas putida biotype B.

    abstract::Ketosteroid isomerase (KSI) from Pseudomonas putida biotype B is a homodimeric enzyme catalyzing an allylic rearrangement of Delta5-3-ketosteroids at rates comparable with the diffusion-controlled limit. The tyrosine triad (Tyr14.Tyr55.Tyr30) forming a hydrogen-bond network in the apolar active site of KSI has been ch...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi015547k

    authors: Nam GH,Jang DS,Cha SS,Lee TH,Kim DH,Hong BH,Yun YS,Oh BH,Choi KY

    更新日期:2001-11-13 00:00:00

  • Multiple forms of phosphodeoxyribomutase from Escherichia coli. Physical and chemical characterization.

    abstract::Phosphodeoxyribomutase from Escherichia coli has been purified to homogeneity. Chromatography on DEAE-Sephadex revealed three peaks of enzyme activity, designated form I, form II, and form III. Form III could be further separated into form III-1 and form III-2 by polyacrylamide gel electrophoresis. The four different ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00674a021

    authors: Leer JC,Hammer-Jespersen K

    更新日期:1975-02-11 00:00:00

  • Vitamin K dependent carboxylase: subcellular location of the carboxylase and enzymes involved in vitamin K metabolism in rat liver.

    abstract::Vitamin K dependent carboxylation of an exogenous peptide substrate and endogenous protein substrates, vitamin K epoxidation, and reduction of vitamin K epoxide were measured in subcellular fractions from rat liver. The rough microsomal fraction was highly enriched in all four activities; lower levels were found in sm...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00547a019

    authors: Carlisle TL,Suttie JW

    更新日期:1980-03-18 00:00:00

  • High-efficiency triple-helix-mediated photo-cross-linking at a targeted site within a selectable mammalian gene.

    abstract::Targeting damage to specific sites in the genome represents an attractive approach to manipulating gene function in mammalian cells. To test the applicability of triple-helix formation as a means for achieving precisely timed site-specific damage within a mammalian gene, a triplex-forming oligodeoxyribonucleotide (TFO...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960881f

    authors: Vasquez KM,Wensel TG,Hogan ME,Wilson JH

    更新日期:1996-08-20 00:00:00

  • Biosynthesis of GDP-d-glycero-α-d-manno-heptose for the Capsular Polysaccharide of Campylobacter jejuni.

    abstract::The capsular polysaccharide (CPS) structure of Campylobacter jejuni contributes to its robust fitness. Many strains contain heptose moieties in their CPS units. The precursor heptose is GDP-d-glycero-α-d-manno-heptose; modifications to the stereochemistry at C3-C6 as well as additions of methyl and phosphoramidate gro...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.9b00548

    authors: Huddleston JP,Raushel FM

    更新日期:2019-09-17 00:00:00

  • Transient aggregation and stable dimerization induced by introducing an Alzheimer sequence into a water-soluble protein.

    abstract::Transient contacts between denatured polypeptide chains are likely to play an important part in the initial stages of protein aggregation and fibrillation. To analyze the nature of such contacts, we have carried out a protein engineering study of the 102-residue protein U1A, which aggregates transiently in the wild-ty...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi048509k

    authors: Otzen DE,Miron S,Akke M,Oliveberg M

    更新日期:2004-10-19 00:00:00

  • Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase.

    abstract::Allosteric activators are generally believed to shift the equilibrium distribution of enzyme conformations to favor a catalytically productive structure; the kinetics of conformational exchange is seldom addressed. Several observations suggested that the usual allosteric mechanism might not apply to the activation of ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200785s

    authors: Riera TV,Zheng L,Josephine HR,Min D,Yang W,Hedstrom L

    更新日期:2011-10-04 00:00:00

  • Phase-resolved spectral measurements with several two tryptophan containing proteins.

    abstract::We have used frequency domain fluorescence techniques to resolve the component emission spectra for several two tryptophan containing proteins (e.g., horse liver alcohol dehydrogenase, sperm whale apomyoglobin, yeast 3-phosphoglycerate kinase, apoazurin from Alcaligenes denitricans). We have first performed multifrequ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00399a047

    authors: Eftink MR,Wasylewski Z,Ghiron CA

    更新日期:1987-12-15 00:00:00

  • Characterization of a cloned human dihydrotestosterone/androstanediol UDP-glucuronosyltransferase and its comparison to other steroid isoforms.

    abstract::A human cDNA, UDPGTh-3, encoding a dihydrotestosterone/5 alpha-androstane-3 alpha,17 beta-diol UDP- glucuronosyltransferase (transferase) has been isolated and characterized. The nucleotide sequence of UDPGTh-3 encodes a 530 amino acid protein with a typical membrane insertion-signal peptide, a membrane-anchoring doma...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00091a015

    authors: Chen F,Ritter JK,Wang MG,McBride OW,Lubet RA,Owens IS

    更新日期:1993-10-12 00:00:00

  • Full-length human glutaminase in complex with an allosteric inhibitor.

    abstract::Glutaminase (GLS1/2) catalyzes the conversion of L-glutamine to L-glutamate and ammonia. The level of a splice variant of GLS1 (GAC) is elevated in certain cancers, and GAC is specifically inhibited by bis-2-(5-phenylacetimido-1,2,4,thiadiazol-2-yl)ethyl sulfide (BPTES). We report here the first full-length crystal st...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi201613d

    authors: DeLaBarre B,Gross S,Fang C,Gao Y,Jha A,Jiang F,Song J J,Wei W,Hurov JB

    更新日期:2011-12-20 00:00:00

  • Mutant IDH1 enhances the production of 2-hydroxyglutarate due to its kinetic mechanism.

    abstract::The human, cytosolic enzyme isocitrate dehydrogenase 1 (IDH1) reversibly converts isocitrate to α-ketoglutarate (αKG). Cancer-associated somatic mutations in IDH1 result in a loss of this normal function but a gain in a new or neomorphic ability to convert αKG to the oncometabolite 2-hydroxyglutarate (2HG). To improve...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi400514k

    authors: Rendina AR,Pietrak B,Smallwood A,Zhao H,Qi H,Quinn C,Adams ND,Concha N,Duraiswami C,Thrall SH,Sweitzer S,Schwartz B

    更新日期:2013-07-02 00:00:00

  • Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.

    abstract::During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism might involve a pentacoordinated zinc or a double-displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast AD...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00446

    authors: Plapp BV,Savarimuthu BR,Ferraro DJ,Rubach JK,Brown EN,Ramaswamy S

    更新日期:2017-07-18 00:00:00

  • Role of mixed oxidation states in the oxidation of hemerythrin species by ferricyanide ion.

    abstract::The oxidation of deoxy- and oxyhemerythrin to methemerythrin by Fe(CN)6(3-) has been examined. The first step produces (semi-met)O, a half-oxidized form of hemerythrin which has different spectral and kinetic properties from (semi-met)R which is produced by one-electron reduction of methemerythrin. Further oxidation o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00559a003

    authors: Bradić Z,Harrington PC,Wilkins RG,Yoneda G

    更新日期:1980-09-02 00:00:00

  • Characterization of multiple forms of the Ah receptor: recognition of a dioxin-responsive enhancer involves heteromer formation.

    abstract::We have employed a combination of gel retardation, protein-DNA cross-linking, and protein-protein cross-linking techniques to further examine the 2,3,7,8-tetrachlorodibenzo-p- dioxin-(TCDD-) dependent changes in the Ah receptor that result in a DNA-binding conformation. Gel retardation analysis of DNA-Sepharose chroma...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00225a026

    authors: Gasiewicz TA,Elferink CJ,Henry EC

    更新日期:1991-03-19 00:00:00

  • Scaffold/matrix-attached regions act upon transcription in a context-dependent manner.

    abstract::Scaffold/matrix-attached regions (S/MARs) are cis-acting elements with a function outside transcribed regions and in introns. Although they usually augment transcriptional rates, their action is highly context-dependent. We cloned an 800 bp S/MAR element from the upstream border of the human interferon-beta domain at ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960930o

    authors: Schübeler D,Mielke C,Maass K,Bode J

    更新日期:1996-08-27 00:00:00

  • Cytochrome P-450 inactivation: structure of the prosthetic heme adduct with propyne.

    abstract::Hepatic microsomal cytochrome P-450 from phenobarbital-pretreated rats is destroyed by propyne in a reduced nicotinamide adenine dinucleotide dependent process which also results in vivo in the accumulation of an abnormal green porphyrin. The green porphyrin has been identified by its electronic absorption, mass spect...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00528a033

    authors: Ortiz de Montellano PR,Kunze KL

    更新日期:1981-12-08 00:00:00

  • Detection of a water molecule in the active-site of bacteriorhodopsin: hydrogen bonding changes during the primary photoreaction.

    abstract::FTIR-difference spectroscopy in combination with site-directed mutagenesis has been used to investigate the role of water during the photocycle of bacteriorhodopsin. At least one water molecule is detected which undergoes an increase in H-bonding during the primary bR-->K phototransition. Bands due to water appear in ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00209a005

    authors: Fischer WB,Sonar S,Marti T,Khorana HG,Rothschild KJ

    更新日期:1994-11-01 00:00:00

  • Tetrahydrobiopterin-free neuronal nitric oxide synthase: evidence for two identical highly anticooperative pteridine binding sites.

    abstract::The properties of neuronal nitric oxide synthase containing one tetrahydrobiopterin (BH4) per dimer [nNOS(BH4+)] were compared to those of the BH4-free enzyme [nNOS(BH4-)]. The stimulation by BH4 of the formation of L-citrulline at the expense of H2O2 production unambiguously demonstrated that BH4 is essential in coup...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi961931j

    authors: Gorren AC,List BM,Schrammel A,Pitters E,Hemmens B,Werner ER,Schmidt K,Mayer B

    更新日期:1996-12-24 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