Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants.

Abstract:

:Heme-derived linear tetrapyrroles (phytobilins) in phycobiliproteins and phytochromes perform critical light-harvesting and light-sensing roles in oxygenic photosynthetic organisms. A key enzyme in their biogenesis, phycocyanobilin:ferredoxin oxidoreductase (PcyA), catalyzes the overall four-electron reduction of biliverdin IXalpha to phycocyanobilin--the common chromophore precursor for both classes of biliproteins. This interconversion occurs via semireduced bilin radical intermediates that are profoundly stabilized by selected mutations of two critical catalytic residues, Asp105 and His88. To understand the structural basis for this stabilization and to gain insight into the overall catalytic mechanism, we report the high-resolution crystal structures of substrate-loaded Asp105Asn and His88Gln mutants of Synechocystis sp. PCC 6803 PcyA in the initial oxidized and one-electron reduced radical states. Unlike wild-type PcyA, both mutants possess a bilin-interacting axial water molecule that is ejected from the active site upon formation of the enzyme-bound neutral radical complex. Structural studies of both mutants also show that the side chain of Glu76 is unfavorably located for D-ring vinyl reduction. On the basis of these structures and companion (15)N-(1)H long-range HMQC NMR analyses to assess the protonation state of histidine residues, we propose a new mechanistic scheme for PcyA-mediated reduction of both vinyl groups of biliverdin wherein an axial water molecule, which prematurely binds and ejects from both mutants upon one electron reduction, is required for catalytic turnover of the semireduced state.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Kohler AC,Gae DD,Richley MA,Stoll S,Gunn A,Lim S,Martin SS,Doukov TI,Britt RD,Ames JB,Lagarias JC,Fisher AJ

doi

10.1021/bi100728q

subject

Has Abstract

pub_date

2010-07-27 00:00:00

pages

6206-18

issue

29

eissn

0006-2960

issn

1520-4995

journal_volume

49

pub_type

杂志文章
  • Diepoxybutane cross-links DNA at 5'-GNC sequences.

    abstract::Epoxides are cancer-causing agents chemically analogous to the nitrogen mustards, a family of powerful antitumor drugs. We found that the DNA interstrand cross-linking sequence preference of diepoxybutane is the same as that of the mustard mechlorethamine: 5'-GNC. Therefore, the genomic site of cross-linking alone can...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00059a034

    authors: Millard JT,White MM

    更新日期:1993-03-02 00:00:00

  • Selection and characterization of a new class of peptide exosite inhibitors of coagulation factor VIIa.

    abstract::A new series of peptide inhibitors of human Factor VIIa (FVIIa) has been identified and affinity matured from naive and partially randomized peptide phage libraries selected against the immobilized tissue factor x Factor VIIa (TF x FVIIa) complex. These "A-series" peptides contain a single disulfide bond and a 13-resi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010591l

    authors: Dennis MS,Roberge M,Quan C,Lazarus RA

    更新日期:2001-08-14 00:00:00

  • The divalent cation is obligatory for the binding of ligands to the catalytic site of secreted phospholipase A2.

    abstract::The divalent cation requirement for partial reactions of the catalytic turnover cycle during interfacial catalysis by pig pancreatic phospholipase A2 (PLA2) is investigated. Results show that the specific role of calcium in all the events of the catalytic cycle at the active site is not shared by other divalent cation...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00076a024

    authors: Yu BZ,Berg OG,Jain MK

    更新日期:1993-06-29 00:00:00

  • Novel benzimidazole inhibitors bind to a unique site in the kinesin spindle protein motor domain.

    abstract::Affinity selection-mass spectrometry (AS-MS) screening of kinesin spindle protein (KSP) followed by enzyme inhibition studies and temperature-dependent circular dichroism (TdCD) characterization was utilized to identify a series of benzimidazole compounds. This series also binds in the presence of Ispinesib, a known a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi1005283

    authors: Sheth PR,Shipps GW Jr,Seghezzi W,Smith CK,Chuang CC,Sanden D,Basso AD,Vilenchik L,Gray K,Annis DA,Nickbarg E,Ma Y,Lahue B,Herbst R,Le HV

    更新日期:2010-09-28 00:00:00

  • Reversal of negative charges on the surface of Escherichia coli thioredoxin: pockets versus protrusions.

    abstract::Recent studies of proteins with reversed charged residues have demonstrated that electrostatic interactions on the surface can contribute significantly to protein stability. We have used the approach of reversing negatively charged residues using Arg to evaluate the effect of the electrostatics context on the transiti...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0354684

    authors: Mancusso R,Cruz E,Cataldi M,Mendoza C,Fuchs J,Wang H,Yang X,Tasayco ML

    更新日期:2004-04-06 00:00:00

  • Specificity determinants on Cdc42 for binding its effector protein ACK.

    abstract::Cdc42 and Rac are highly homologous members of the Rho family of small G proteins that interact with several downstream effector proteins thereby causing cytoskeletal rearrangements, cell proliferation, and differentiation. While some effectors, such as the tyrosine kinase, ACK, and the scaffold protein, WASP, are uni...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0506021

    authors: Elliot-Smith AE,Mott HR,Lowe PN,Laue ED,Owen D

    更新日期:2005-09-20 00:00:00

  • Molecular dynamics simulations of binding modes between methylene blue and DNA with alternating GC and AT sequences.

    abstract::The understanding of interactions between small molecules and DNA is crucial to design new anticancer drugs targeted to DNA. Methylene blue (MB) is a phenothiazinium dye that has shown promising results in photodynamic therapy treatment. The noncovalent binding of methylene blue to DNA was experimentally and theoretic...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500068z

    authors: Nogueira JJ,González L

    更新日期:2014-04-15 00:00:00

  • Structure and polymorphism of saturated monoacid 1,2-diacyl-sn-glycerols.

    abstract::The 1,2-diacyl-sn-glycerols (1,2-DGs) are the predominant naturally occurring isomer found in cell membranes, lipid droplets, and lipoproteins. They are involved in the metabolism of monoacylglycerols, triacylglycerols, and phospholipids. The 1,2-DGs participate in the activation of protein kinase C, in phosphorylatio...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00500a008

    authors: Kodali DR,Fahey DA,Small DM

    更新日期:1990-12-04 00:00:00

  • Refinement of the solution structure of the DNA dodecamer 5'd(CGCGPATTCGCG)2 containing a stable purine-thymine base pair: combined use of nuclear magnetic resonance and restrained molecular dynamics.

    abstract::The solution structure of the self-complementary dodecamer 5'd(CGCGPATTCGCG)2, containing a purine-thymine base pair within the hexameric canonical recognition site GAATTC for the restriction endonuclease EcoRI, is investigated by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Nonexchangeab...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00411a042

    authors: Clore GM,Oschkinat H,McLaughlin LW,Benseler F,Happ CS,Happ E,Gronenborn AM

    更新日期:1988-05-31 00:00:00

  • Molecular characterization of limulin, a sialic acid binding lectin from the hemolymph of the horseshoe crab, Limulus polyphemus.

    abstract::The sialic acid binding lectin, limulin, was isolated by gel filtration and ion-exchange chromatography from the hemolymph of Limulus polyphemus. When the purified protein was characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the presence of beta-mercaptoethanol, two major protein bands wer...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00638a026

    authors: Kaplan R,Li SS,Kehoe JM

    更新日期:1977-09-20 00:00:00

  • Interaction of a paramagnetic analogue of oxaloacetate with citrate synthase.

    abstract::Electron paramagnetic resonance studies have indicated that nitrosodisulfonate binds to pig heart citrate synthase. Titration of the enzyme with nitrosodisulfonate revealed several binding sites for the probe per subunit with one site (KD approximately 0.1 mM) having a greater affinity than the others. The substrate, ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00584a028

    authors: Weidman SW,Drysdale GR

    更新日期:1979-08-21 00:00:00

  • Cyclopiazonic acid biosynthesis in Aspergillus sp.: characterization of a reductase-like R* domain in cyclopiazonate synthetase that forms and releases cyclo-acetoacetyl-L-tryptophan.

    abstract::The fungal neurotoxin alpha-cyclopiazonic acid (CPA), a nanomolar inhibitor of Ca2+-ATPase, has a pentacyclic indole tetramic acid scaffold that arises from one molecule of tryptophan, acetyl-CoA, malonyl-CoA, and dimethylallyl pyrophosphate by consecutive action of three enzymes, CpaS, CpaD, and CpaO. CpaS is a hybri...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi901123r

    authors: Liu X,Walsh CT

    更新日期:2009-09-15 00:00:00

  • Inhibition of NAD(P)H:(quinone-acceptor) oxidoreductase by cibacron blue and related anthraquinone dyes: a structure-activity study.

    abstract::Cibacron Blue, a widely used ligand for affinity chromatography, is a potent inhibitor of NAD(P)H:(quinone-acceptor) oxidoreductase (EC 1.6.99.2) (quinone reductase). This property has been exploited to purify quinone reductase, to identify its nucleotide-binding site, and to obtain diffraction-grade crystals of this ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00118a027

    authors: Prestera T,Prochaska HJ,Talalay P

    更新日期:1992-01-28 00:00:00

  • Histone H2A phosphorylation in animal cells: functional considerations.

    abstract::We have sought to determine the role of histone H2A phosphorylation in chromatin by examining the distribution of the phosphorylated and unphosphorylated forms of this core histone within the nuclei of mouse and human cells. At any time, only about 15% of the H2A of whole chromatin is in the phosphorylated form, and i...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00539a021

    authors: Prentice DA,Loechel SC,Kitos PA

    更新日期:1982-05-11 00:00:00

  • Arginine294 is essential for the inhibition of Anabaena PCC 7120 ADP-glucose pyrophosphorylase by phosphate.

    abstract::Treatment of ADP-glucose pyrophosphorylase (EC 2.7.7.27) from the cyanobacterium Anabaena PCC 7120 with phenylglyoxal in 50 mM Hepes, pH 8.0, at 25 degrees C resulted in a time- and concentration-dependent loss of enzyme activity. Phosphate, the inhibitor, protected the enzyme from inactivation most effectively, while...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9713355

    authors: Sheng J,Preiss J

    更新日期:1997-10-21 00:00:00

  • Role of the linker region connecting the reductase and heme domains in cytochrome P450BM-3.

    abstract::Cytochrome P450BM-3 is a fatty acid monooxygenase that contains the catalytic P450 heme domain covalently attached to a diflavin P450 reductase domain. The function of the linker region connecting the C-terminal end of the heme domain to the N-terminal end of the reductase domain has been studied by deleting parts of ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00035a031

    authors: Govindaraj S,Poulos TL

    更新日期:1995-09-05 00:00:00

  • Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member.

    abstract::MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial acti...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200877x

    authors: Li HJ,Li X,Liu N,Zhang H,Truglio JJ,Mishra S,Kisker C,Garcia-Diaz M,Tonge PJ

    更新日期:2011-11-08 00:00:00

  • Steric constraints in the retinal binding pocket of sensory rhodopsin I.

    abstract::Steric constraints in the retinal binding pocket of sensory rhodopsin I (SR-I) are analyzed by studying effects of sample temperature and retinal analogs. The flash-induced yield of the earliest detected intermediate S610, which corresponds to the K intermediate in the bacteriorhodopsin (BR) photocycle, decreases belo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00089a044

    authors: Yan B,Xie A,Nienhaus GU,Katsuta Y,Spudich JL

    更新日期:1993-09-28 00:00:00

  • Circular substrates of the hammerhead ribozyme shift the internal equilibrium further toward cleavage.

    abstract::To test whether the Y-shaped conformation of the hammerhead ribozyme is maintained throughout the catalytic pathway, the cleavage properties of circular substrates which bind the ribozyme through helices I and II were determined. Constraining the position of helices I and II in this manner did not significantly alter ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980307z

    authors: Stage-Zimmermann TK,Uhlenbeck OC

    更新日期:1998-06-30 00:00:00

  • Solution structure of the paramagnetic complex of the N-terminal domain of calmodulin with two Ce3+ ions by 1H NMR.

    abstract::The solution structure of the dicerium(III) complex of the N-terminal domain of calmodulin (Ce2-TR1C hereafter) has been solved employing paramagnetic T1 relaxation enhancements and pseudocontact shifts introduced by the Ce3+ ions, together with conventional NOE constraints. The use of pseudocontact shift constraints ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971022+

    authors: Bentrop D,Bertini I,Cremonini MA,Forsén S,Luchinat C,Malmendal A

    更新日期:1997-09-30 00:00:00

  • Sulfide dehydrogenase activity of the monomeric flavoprotein SoxF of Paracoccus pantotrophus.

    abstract::Flavocytochrome c-sulfide dehydrogenases (FCSDs) are complexes of a flavoprotein with a c-type cytochrome performing hydrogen sulfide-dependent cytochrome c reduction in vitro. The amino acid sequence analysis revealed that the phylogenetic relationship of different flavoproteins reflected the relationship of sulfur-o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi048568y

    authors: Quentmeier A,Hellwig P,Bardischewsky F,Wichmann R,Friedrich CG

    更新日期:2004-11-23 00:00:00

  • How fumarase recycles after the malate --> fumarate reaction. Insights into the reaction mechanism.

    abstract::Recycling of yeast fumarase to permit repetition of its reaction chemistry requires two proton transfers and two conformational changes, in pathways that are different in detail but thematically similar in the two directions. In the malate --> fumarate direction, simple anions such as acetate accelerate the fumarate-o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9821521

    authors: Rose IA

    更新日期:1998-12-22 00:00:00

  • Klenow fragment-DNA interaction required for the incorporation of nucleotides opposite guanine and O6-methylguanine.

    abstract::A mechanism by which the Klenow fragment of DNA polymerase I monitors the geometry of the base pairs may involve hydrogen bonds between the polymerase and the minor groove of the nascent base pair. The involvement of the 3-position of guanine in the template strand was examined by synthesizing oligodeoxynucleotides co...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971253g

    authors: Spratt TE

    更新日期:1997-10-28 00:00:00

  • H-Ras peptide and protein substrates bind protein farnesyltransferase as an ionized thiolate.

    abstract::The zinc metalloenzyme protein farnesyltransferase (FTase) catalyzes the alkylation of a cysteine residue of protein substrates with a 15 carbon farnesyl group. We have developed fluorescence assays to directly measure the affinity of the enzyme for peptide and protein (Ras) substrates. A peptide corresponding to the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi981525v

    authors: Hightower KE,Huang CC,Casey PJ,Fierke CA

    更新日期:1998-11-03 00:00:00

  • The interface between the EGF2 domain and the protease domain in blood coagulation factor IX contributes to factor VIII binding and factor X activation.

    abstract::The light chain of activated factor IX (FIXa) is involved in a number of functional properties, including FIXa enzymatic activity. This suggests the existence of a functional link between the FIXa light chain and the catalytic domain. The FIXa structure includes a few putative interactions between EGF2 and the proteas...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi060451h

    authors: Fribourg C,Meijer AB,Mertens K

    更新日期:2006-09-05 00:00:00

  • Action of antimicrobial peptides: two-state model.

    abstract::The argument and experimental evidence are presented for a two-state model that explains the action of both helical and beta-sheet antimicrobial peptides after they bind to the plasma membranes of cells. Each peptide has two distinct physical states of binding to lipid bilayers. At low peptide-to-lipid ratios (P/L), t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000946l

    authors: Huang HW

    更新日期:2000-07-25 00:00:00

  • Characterization of a small metal binding protein from Nitrosomonas europaea.

    abstract::A small metal-binding protein (SmbP) with no known similarity to other proteins in current databases was isolated and characterized from the periplasm of Nitrosomonas europaea. The primary structure of this small (9.9 kDa) monomeric protein is characterized by a series of 10 repeats of a seven amino acid motif and an ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049318k

    authors: Barney BM,LoBrutto R,Francisco WA

    更新日期:2004-09-07 00:00:00

  • Modulation of the actin-activated adenosinetriphosphatase activity of myosin by tropomyosin from vascular and gizzard smooth muscles.

    abstract::Tropomyosins from bovine aorta and pulmonary artery exhibit identical electrophoretic patterns in sodium dodecyl sulfate but differ from tropomyosins of either chicken gizzard or rabbit skeletal muscle. Each of the four tropomyosins binds readily to skeletal muscle F-actin as indicated by their sedimentation with acti...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00299a029

    authors: Yamaguchi M,Ver A,Carlos A,Seidel JC

    更新日期:1984-02-14 00:00:00

  • Bioluminescence of beetle luciferases with 6'-amino-D-luciferin analogues reveals excited keto-oxyluciferin as the emitter and phenolate/luciferin binding site interactions modulate bioluminescence colors.

    abstract::Beetle luciferases produce different bioluminescence colors from green to red using the same d-luciferin substrate. Despite many studies of the mechanisms and structural determinants of bioluminescence colors with firefly luciferases, the identity of the emitters and the specific active site interactions responsible f...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500160m

    authors: Viviani VR,Neves DR,Amaral DT,Prado RA,Matsuhashi T,Hirano T

    更新日期:2014-08-19 00:00:00

  • Isolation and characterization of neutralizing single-chain antibodies against Xenopus mitogen-activated protein kinase kinase from phage display libraries.

    abstract::MAP kinase kinase (MAPKK) is a dual specificity protein kinase that phosphorylates and activates MAP kinase in vivo. In this study, four mouse monoclonal single-chain Fv (scFv) antibodies (Y1-6, Y1-7, Y3-6, and Y3-11) that can specifically bind to Xenopus MAPKK were isolated from combinatorial scFv-displaying phage li...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960956f

    authors: Kosako H,Akamatsu Y,Tsurushita N,Lee KK,Gotoh Y,Nishida E

    更新日期:1996-10-08 00:00:00