Completely buried, non-ion-paired glutamic acid contributes favorably to the conformational stability of pyrrolidone carboxyl peptidases from hyperthermophiles.

Abstract:

:Pyrrolidone carboxyl peptidases (PCPs) from hyperthermophiles have a structurally conserved and completely buried Glu192 in the hydrophobic core; in contrast, the corresponding residue in the mesophile protein is a hydrophobic residue, Ile. Does the buried ionizable residue contribute to stabilization or destabilization of hyperthermophile PCPs? To elucidate the role of the buried glutamic acid in stabilizing PCP from hyperthermophiles, we constructed five Glu192 mutants of PCP-0SH (C142S/C188S, Cys-free double mutant of PCP) from Pyrococcus furiosus and examined their thermal and pH-induced unfolding and crystal structures and compared them with those of PCP-0SH. The stabilities of apolar (E192A/I/V) and polar (E192D/Q) mutants were less than PCP-0SH at acidic pH values. In the alkaline region, the mutant proteins, except for E192D, were more stable than PCP-0SH. The thermal stability data and theoretical calculations indicated an apparent pKa value > or = 7.3 for Glu192. Present results confirmed that the protonated Glu192 in PCP-0SH forms strong hydrogen bonds with the carbonyl oxygen and peptide nitrogen of Pro168. New intermolecular hydrogen bonds in the E --> A/D mutants were formed by a water molecule introduced into the cavity created around position 192, whereas the hydrogen bonds disappeared in the E --> I/V mutants. Structure-based empirical stability of mutant proteins was in good agreement with the experimental results. The results indicated that (1) completely buried Glu192 contributes to the stabilization of PCP-0SH because of the formation of strong intramolecular hydrogen bonds and (2) the hydrogen bonds by the nonionized and buried Glu can contribute more than the burial of hydrophobic groups to the conformational stability of proteins.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Kaushik JK,Iimura S,Ogasahara K,Yamagata Y,Segawa S,Yutani K

doi

10.1021/bi052610n

subject

Has Abstract

pub_date

2006-06-13 00:00:00

pages

7100-12

issue

23

eissn

0006-2960

issn

1520-4995

journal_volume

45

pub_type

杂志文章
  • Catalase HPII from Escherichia coli exhibits enhanced resistance to denaturation.

    abstract::Catalase HPII from Escherichia coli is a homotetramer of 753 residue subunits. The multimer displays a number of unusual structural features, including interwoven subunits and a covalent bond between Tyr415 and His392, that would contribute to its rigidity and stability. As the temperature of a solution of HPII in 50 ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi982863z

    authors: Switala J,O'Neil JO,Loewen PC

    更新日期:1999-03-30 00:00:00

  • Solution structure of the Dickerson DNA dodecamer containing a single ribonucleotide.

    abstract::Ribonucleotides are frequently incorporated into DNA during replication. They are recognized and processed by several cellular enzymes, and their continued presence in the yeast nuclear genome results in replicative stress and genome instability. Thus, it is important to understand the effects of isolated ribonucleoti...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi201710q

    authors: DeRose EF,Perera L,Murray MS,Kunkel TA,London RE

    更新日期:2012-03-27 00:00:00

  • Fate of the (2Fe-2S)(2+) cluster of Escherichia coli biotin synthase during reaction: a Mössbauer characterization.

    abstract::Biotin synthase, the enzyme which catalyzes the last step of the biosynthesis of biotin, contains only (2Fe-2S)(2+) clusters when isolated under aerobic conditions. Previous results showed that reduction by dithionite or photoreduced deazaflavin converts the (2Fe-2S)(2+) to (4Fe-4S)(2+,+). However, until now, no detai...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi034426c

    authors: Tse Sum Bui B,Benda R,Schünemann V,Florentin D,Trautwein AX,Marquet A

    更新日期:2003-07-29 00:00:00

  • Characterization of Natural Colibactin-Nucleobase Adducts by Tandem Mass Spectrometry and Isotopic Labeling. Support for DNA Alkylation by Cyclopropane Ring Opening.

    abstract::Colibactins are genotoxic secondary metabolites whose biosynthesis is encoded in the clb gene cluster harbored by certain strains of gut commensal Escherichia coli. Using synthetic colibactin analogues, we previously provided evidence that colibactins alkylate DNA by addition of a nucleotide to an electrophilic cyclop...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b01023

    authors: Xue M,Shine E,Wang W,Crawford JM,Herzon SB

    更新日期:2018-11-13 00:00:00

  • Role of the covalent flavin linkage in monomeric sarcosine oxidase.

    abstract::Monomeric sarcosine oxidase (MSOX) is a prototypical member of a recently recognized family of amine-oxidizing enzymes that all contain covalently bound flavin. Mutation of the covalent flavin attachment site in MSOX produces a catalytically inactive apoprotein (apoCys315Ala) that forms an unstable complex with FAD (K...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0607352

    authors: Hassan-Abdallah A,Zhao G,Jorns MS

    更新日期:2006-08-08 00:00:00

  • Mapping the interfacial binding surface of human secretory group IIa phospholipase A2.

    abstract::Human secretory group IIa phospholipase A2 (hIIa-PLA2) contains a large number of prominent cationic patches on its molecular surface and has exceptionally high affinity for anionic surfaces, including anionic membranes. To identify the cationic amino acid residues that support binding of hIIa-PLA2 to anionic membrane...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971200z

    authors: Snitko Y,Koduri RS,Han SK,Othman R,Baker SF,Molini BJ,Wilton DC,Gelb MH,Cho W

    更新日期:1997-11-25 00:00:00

  • Gross structural changes in isolated liver cell plasma membranes upon binding of insulin.

    abstract::The addition of 10(-9) M insulin to a suspension of rat liver plasma membranes increases the overall lipid microviscosity, eta, by about 10--20%. The effect is confined to physiological concentrations of the hormone and is highly specific. The specificity was demonstrated in experiments where insulin analogues were ad...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00570a009

    authors: Luly P,Shinitzky M

    更新日期:1979-02-06 00:00:00

  • Estimation of the distance change between cysteine-457 and the nucleotide binding site when sodium pump changes conformation from E1 to E2 by fluorescence energy transfer measurements.

    abstract::The first indication of the size of a conformational change implicated in ion transport by sodium pump has been obtained by measuring the change in efficiency of fluorescence energy transfer between two specific locations on the alpha-subunit. The donor (5'-(iodoacetamido)fluorescein) attaches covalently to cysteine-4...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960407+

    authors: Lin SH,Faller LD

    更新日期:1996-06-25 00:00:00

  • Kinetics of the subtransition of asymmetrically substituted phosphatidylcholines.

    abstract::The thermodynamics and kinetics of the subtransition L epsilon----P beta of sonicated unilamellar vesicles of 1-myristoyl-2-stearoylphosphatidylcholine (1M-2S-PC) and of 1-stearoyl-2-myristoylphosphatidylcholine (1S-2M-PC) were studied by equilibrium cooling curves and temperature-jump relaxation spectrometry with an ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00313a009

    authors: Tümmler B,Herrmann U,Maass G,Eibl H

    更新日期:1984-08-28 00:00:00

  • A-tract polarity dominate the curvature in flanking sequences.

    abstract::It is well-known, but little understood, that the nucleotide sequences between phased A(4-6)-tracts (at 10-11 bp intervals) have only a slight effect on overall curvature. To explore this phenomenon, we have examined the gel-migration properties of sequences containing both A-tracts as well as G-tracts (i.e., sequence...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi020662w

    authors: Merling A,Sagaydakova N,Haran TE

    更新日期:2003-05-06 00:00:00

  • In Situ Photoregulation of Carbonic Anhydrase Activity Using Azobenzenesulfonamides.

    abstract::We report two small molecule azobenzenesulfonamide probes, CAP1 and CAP2, capable of photomodulating the activity of carbonic anhydrase (CA) on demand. In the trans form, CAP azobenzene probes adopt a linear shape, making them suitable for occupying the CA active site and interacting with Zn2+, thereby inhibiting enzy...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b00947

    authors: Aggarwal K,Banik M,Medellin B,Que EL

    更新日期:2019-01-08 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

  • Inactivation of C30A trimethylamine dehydrogenase by N-cyclopropyl-alpha-methylbenzylamine, 1-phenylcyclopropylamine, and phenylhydrazine.

    abstract::Trimethylamine dehydrogenase (TMADH) from the bacterium Methylophilus methylotrophus (sp. W(3)A(1)) and its C30A mutant were inactivated with three known inactivators of monoamine oxidase, namely, phenylhydrazine, N-cyclopropyl-alpha-methylbenzylamine, and 1-phenylcyclopropylamine. All three compounds irreversibly ina...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0105126

    authors: Mitchell DJ,Nikolic D,Jang MH,van Breemen RB,Hille R,Silverman RB

    更新日期:2001-07-24 00:00:00

  • An engineered disulfide bond in dihydrofolate reductase.

    abstract::Substitution of cysteine for proline-39 in Escherichia coli dihydrofolate reductase by oligonucleotide-directed mutagenesis positions the new cysteine adjacent to already existing cysteine-85. When the mutant protein is expressed in the E. coli cytosol, the cysteine sulfur atoms are found, by X-ray crystallographic an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00382a017

    authors: Villafranca JE,Howell EE,Oatley SJ,Xuong NH,Kraut J

    更新日期:1987-04-21 00:00:00

  • An Efficient Viologen-Based Electron Donor to Nitrogenase.

    abstract::Nitrogenase catalyzes the reduction of N2 to NH3, supporting all biological nitrogen fixation. Electron donors to this enzyme are ferredoxin or flavodoxin (in vivo) and sodium dithionite (in vitro). Features of these electron donors put a limit on spectrophotometric studies and electrocatalytic applications of nitroge...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.9b00844

    authors: Badalyan A,Yang ZY,Hu B,Luo J,Hu M,Liu TL,Seefeldt LC

    更新日期:2019-11-19 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

  • Regulation of the expression of the β-lactam antibiotic-resistance determinants in methicillin-resistant Staphylococcus aureus (MRSA).

    abstract::β-Lactam antibiotics have faced obsolescence with the emergence of methicillin-resistant Staphylococcus aureus (MRSA). A complex set of events ensues upon exposure of MRSA to these antibiotics, which culminates in proteolysis of BlaI or MecI, two gene repressors, and results in the induction of resistance. We report s...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500074w

    authors: Blázquez B,Llarrull LI,Luque-Ortega JR,Alfonso C,Boggess B,Mobashery S

    更新日期:2014-03-18 00:00:00

  • Properties of tetrahydropteroylpentaglutamate bound to 10-formyltetrahydrofolate dehydrogenase.

    abstract::A new rapid procedure for purifying 10-formyltetrahydrofolate dehydrogenase results in 90 mg of pure enzyme from two rabbit livers. This abundant liver enzyme is known to bind its product tetrahydropteroylpentaglutamate (H4PteGlu5) so tightly that it does not dissociate during size exclusion chromatography. 10-Formylt...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9619684

    authors: Kim DW,Huang T,Schirch D,Schirch V

    更新日期:1996-12-10 00:00:00

  • HlyC, the internal protein acyltransferase that activates hemolysin toxin: role of conserved histidine, serine, and cysteine residues in enzymatic activity as probed by chemical modification and site-directed mutagenesis.

    abstract::HlyC is an internal protein acyltransferase that activates hemolysin, a toxic protein produced by pathogenic Escherichia coli. Acyl-acyl carrier protein (ACP) is the essential acyl donor. Separately subcloned, expressed, and purified prohemolysin A (proHlyA), HlyC, and [1-14C]myristoyl-ACP have been used to study the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi982491u

    authors: Trent MS,Worsham LM,Ernst-Fonberg ML

    更新日期:1999-03-16 00:00:00

  • Structure-function relationships in human glutathione-dependent formaldehyde dehydrogenase. Role of Glu-67 and Arg-368 in the catalytic mechanism.

    abstract::The active-site zinc in human glutathione-dependent formaldehyde dehydrogenase (FDH) undergoes coenzyme-induced displacement and transient coordination to a highly conserved glutamate residue (Glu-67) during the catalytic cycle. The role of this transient coordination of the active-site zinc to Glu-67 in the FDH catal...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi052554q

    authors: Sanghani PC,Davis WI,Zhai L,Robinson H

    更新日期:2006-04-18 00:00:00

  • Solid-State Nuclear Magnetic Resonance Structural Study of the Retinal-Binding Pocket in Sodium Ion Pump Rhodopsin.

    abstract::The recently identified Krokinobacter rhodopsin 2 (KR2) functions as a light-driven sodium ion pump. The structure of the retinal-binding pocket of KR2 offers important insights into the mechanisms of KR2, which has motif of Asn112, Asp116, and Gln123 (NDQ) that is common among sodium ion pump rhodopsins but is unique...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00999

    authors: Shigeta A,Ito S,Inoue K,Okitsu T,Wada A,Kandori H,Kawamura I

    更新日期:2017-01-31 00:00:00

  • Sulfide binding properties of truncated hemoglobins.

    abstract::The truncated hemoglobins from Bacillus subtilis (Bs-trHb) and Thermobifida fusca (Tf-trHb) have been shown to form high-affinity complexes with hydrogen sulfide in their ferric state. The recombinant proteins, as extracted from Escherichia coli cells after overexpression, are indeed partially saturated with sulfide, ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi901671d

    authors: Nicoletti FP,Comandini A,Bonamore A,Boechi L,Boubeta FM,Feis A,Smulevich G,Boffi A

    更新日期:2010-03-16 00:00:00

  • Cadmium-113 NMR studies of the DNA binding domain of the mammalian glucocorticoid receptor.

    abstract::The DNA binding domain of the mammalian glucocorticoid hormone receptor (GR) contains nine highly conserved cysteine residues, a conservation shared by the superfamily of steroid and thyroid hormone receptors. A fragment [150 amino acids (AA) in length] consisting of GR residues 407-556, containing within it the entir...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00491a016

    authors: Pan T,Freedman LP,Coleman JE

    更新日期:1990-10-02 00:00:00

  • Interaction of C225SR1 mutant subunit of ribonucleotide reductase with R2 and nucleoside diphosphates: tales of a suicidal enzyme.

    abstract::Ribonucleotide reductase (RDPR) from Escherichia coli is composed of two subunits, R1 and R2, both of which are required to catalyze the conversion of nucleotides to deoxynucleotides. This reduction process is accompanied by oxidation of two cysteines within the active site to a disulfide. One of these putative active...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00155a030

    authors: Mao SS,Holler TP,Bollinger JM Jr,Yu GX,Johnston MI,Stubbe J

    更新日期:1992-10-13 00:00:00

  • Limited proteolysis as a probe of the conformation and nucleic acid binding regions of nucleolin.

    abstract::Nucleolin, also called protein C23, is a RNA-associated protein implicated in the early stages of ribosome assembly. To study the general conformation and map the nucleic acid binding regions, rat nucleolin was subjected to limited proteolysis using trypsin and chymotrypsin in the presence or absence of poly(G). The c...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00476a006

    authors: Olson MO,Kirstein MN,Wallace MO

    更新日期:1990-06-19 00:00:00

  • Conformational Heterogeneity in a Fully Complementary DNA Three-Way Junction with a GC-Rich Branchpoint.

    abstract::DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully complementary 3WJ and found that it contained unpaired bases at the branchpoint, which is consistent with previous observa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00677

    authors: Toulmin A,Baltierra-Jasso LE,Morten MJ,Sabir T,McGlynn P,Schröder GF,Smith BO,Magennis SW

    更新日期:2017-09-19 00:00:00

  • Characterization of myotoxin a from the venom of prairie rattlesnake (Crotalus viridis viridis).

    abstract::A previously unknown polypeptide myotoxin, designated myotoxin a, was isolated for the first time from prairie rattlesnake (Crotalus viridis viridis) venom. Electrophoretic homogeneity of myotoxin a was shown in beta-alanine disc gel polyacrylamide gel electrophoresis and in isoelectric focusing gel electrophoresis. M...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00630a035

    authors: Cameron DL,Tu AT

    更新日期:1977-05-31 00:00:00

  • Structural determination of oligosaccharides derived from lipooligosaccharide of Neisseria gonorrhoeae F62 by chemical, enzymatic, and two-dimensional NMR methods.

    abstract::F62 LOS of Neisseria gonorrhoeae consists of two major LOS components; the higher and smaller molecular weight (MW) components were recognized by MAbs 1-1-M and 3F11 respectively. Base-line separation of the two major oligosaccharide (OS) components from F62 LOS was achieved by Bio-Gel P-4 chromatography after dephosp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00107a028

    authors: Yamasaki R,Bacon BE,Nasholds W,Schneider H,Griffiss JM

    更新日期:1991-10-29 00:00:00

  • Transmembrane topology of mammalian planar cell polarity protein Vangl1.

    abstract::Vangl1 and Vangl2 are membrane proteins that play an important role in neurogenesis, and Vangl1/Vangl2 mutations cause neural tube defects in mice and humans. At the cellular level, Vangl proteins regulate the establishment of planar cell polarity (PCP), a process requiring membrane assembly of asymmetrically distribu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi101767a

    authors: Iliescu A,Gravel M,Horth C,Apuzzo S,Gros P

    更新日期:2011-03-29 00:00:00

  • Evaluation of copper2+ affinities for the prion protein.

    abstract::The prion protein (PrP) is a cell-surface Cu2+ binding glycoprotein which can bind six copper ions. The role of Cu2+ in PrP function, misfolding, and prion disease has generated much interest; however, the field has been hampered by a lack of consensus with regard to the affinity of Cu2+ for PrPC. Here we build on our...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9011397

    authors: Nadal RC,Davies P,Brown DR,Viles JH

    更新日期:2009-09-29 00:00:00