Protein Arginine Methyltransferase 8: Tetrameric Structure and Protein Substrate Specificity.

Abstract:

:Type I protein arginine methyltransferases (PRMTs) catalyze asymmetric dimethylation of various proteins, and their dysregulations often correlate with tumorigenesis or developmental deficiency. Recent studies have focused on the in vivo substrate identification and the enzyme mechanism with peptide substrates. However, how PRMTs recognize substrates at the protein level remains unknown. PRMT8 is one of the least characterized type I PRMTs, and its crystal structure has not been reported. Here, we report the crystal structure of the PRMT8:SAH complex, identify a new non-histone protein substrate NIFK, and uncover a previously unknown regulatory region specifically required for recognizing NIFK. Instead of the canonical dimeric structure for other type I PRMTs, PRMT8 exists as a tetramer in solution. Using X-ray crystallography in combination with small-angle X-ray scattering experiments, the dimer of dimers architecture in which two PRMT8 dimers are held together mainly by β strand interactions was proposed. Mutation of PRMT8-β15 impedes the methylation of NIFK but still allows methylation of the histone H2A/H2B dimer or a peptide substrate, suggesting a possible structural basis for recognition of protein substrates. Lastly, we observed two PRMT8 dimer orientations resulting in open (without SAH) and closed (with SAH bound) conformations. The comparison between open and closed conformations may provide useful information for PRMT1/8 inhibitor design.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Lee WC,Lin WL,Matsui T,Chen ES,Wei TY,Lin WH,Hu H,Zheng YG,Tsai MD,Ho MC

doi

10.1021/acs.biochem.5b00995

subject

Has Abstract

pub_date

2015-12-29 00:00:00

pages

7514-23

issue

51

eissn

0006-2960

issn

1520-4995

journal_volume

54

pub_type

杂志文章
  • Characterization of ribonucleic acid polymerase-T7 promoter binary complexes.

    abstract::Several experimental approaches have been employed to independently determine rates of dissociation for Escherichia coli RNA polymerase from the T7 bacteriophage A1, A2, A3, and D promoters. Heparin challenge measurements employing abortive initiation turnover rates as an index of promoter occupancy were carried out o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00552a023

    authors: Cech CL,McClure WR

    更新日期:1980-05-27 00:00:00

  • Binding of protein synthesis initiation factor 4E to oligoribonucleotides: effects of cap accessibility and secondary structure.

    abstract::The binding of rabbit globin mRNA to the 25-kDa cap binding protein eIF-4E from human erythrocytes was found to be 5.3-fold stronger than the binding of the cap analogue m7GpppG to eIF-4E [Gross et al. (1990) Biochemistry 29, 5008-5012]. In order to investigate whether this effect is due to the longer sequence of nucl...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00120a020

    authors: Carberry SE,Friedland DE,Rhoads RE,Goss DJ

    更新日期:1992-02-11 00:00:00

  • 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 ver...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00238a028

    authors: Karpusas M,Holland D,Remington SJ

    更新日期:1991-06-18 00:00:00

  • Inhibition of peptidyl-prolyl cis/trans isomerase activity by substrate analog structures: thioxo tetrapeptide-4-nitroanilides.

    abstract::The ubiquitous cyclophilins belong to peptidyl-prolyl cis/trans isomerases (PPIases; EC 5.2.1.8). They are able to catalyze the cis/trans isomerization about peptidyl-prolyl amide bonds. The mode of action of human cytosolic cyclophilin (Cyp18cy) has been studied on substrate analog tetrapeptide-4-nitroanilides contai...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00040a012

    authors: Schutkowski M,Wöllner S,Fischer G

    更新日期:1995-10-10 00:00:00

  • Prion protein peptides induce alpha-helix to beta-sheet conformational transitions.

    abstract::The structures of synthetic peptides corresponding to regions of putative secondary structure in the cellular prion protein PrPC were studied as models for the conformational transition that features in the formation of the pathogenic isoform, PrPSc. Transgenetic studies argue that these PrP isoforms interact during t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00013a006

    authors: Nguyen J,Baldwin MA,Cohen FE,Prusiner SB

    更新日期:1995-04-04 00:00:00

  • Analysis of human cytochrome P450 2C8 substrate specificity using a substrate pharmacophore and site-directed mutants.

    abstract::The structural determinants of substrate specificity of human liver cytochrome P450 2C8 (CYP2C8) were investigated using site-directed mutants chosen on the basis of a preliminary substrate pharmacophore and a three-dimensional (3D) model. Analysis of the structural features common to CYP2C8 substrates exhibiting a mi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0489309

    authors: Melet A,Marques-Soares C,Schoch GA,Macherey AC,Jaouen M,Dansette PM,Sari MA,Johnson EF,Mansuy D

    更新日期:2004-12-14 00:00:00

  • Conserved phosphoprotein interaction motif is functionally interchangeable between ataxin-7 and arrestins.

    abstract::Olivopontocerebellar atrophy with retinal degeneration is a hereditary neurodegenerative disorder that belongs to the subtype II of the autosomal dominant cerebellar ataxias and is characterized by early-onset cerebellar and macular degeneration preceded by diagnostically useful tritan colorblindness. The gene mutated...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi992694y

    authors: Mushegian AR,Vishnivetskiy SA,Gurevich VV

    更新日期:2000-06-13 00:00:00

  • Delineation of two functionally distinct gammaPDE binding sites on the bovine retinal cGMP phosphodiesterase by a mutant gammaPDE subunit.

    abstract::The gamma subunit of the retinal cGMP phosphodiesterase (gammaPDE) acts as an inhibitor of phosphodiesterase (PDE) catalytic activity and mediates enzyme regulation by the alpha subunit of the GTP-binding protein transducin (alphaT). In this work, we describe a full length, doubly point-mutated gamma subunit, C68S, Y8...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi981683m

    authors: Berger AL,Cerione RA,Erickson JW

    更新日期:1999-01-26 00:00:00

  • Peptide binding by calmodulin and its proteolytic fragments and by troponin C.

    abstract::Calmodulin and troponin C exhibit calcium-dependent binding of 1 mol/mol of dynorphin. The dissociation constants of the complexes, determined in 0.20 N KC1-1.0 mM CaCI2, pH 7.3, are 0.6 microM for calmodulin, 2.4 microM for rabbit fast skeletal muscle troponin C, and 9 microM for bovine heart troponin C. Experiments ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00306a016

    authors: Malencik DA,Anderson SR

    更新日期:1984-05-22 00:00:00

  • The binding mechanism of pyoverdin with the outer membrane receptor FpvA in Pseudomonas aeruginosa is dependent on its iron-loaded status.

    abstract::In iron-deficient conditions, Pseudomonas aeruginosa secretes a major fluorescent siderophore named pyoverdin (Pvd), which after chelating iron(III) is transported back into the cell via its outer membrane receptor FpvA. FpvA is a TonB-dependent transport protein and has the ability to bind Pvd in its apo- or iron-loa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049768c

    authors: Clément E,Mesini PJ,Pattus F,Schalk IJ

    更新日期:2004-06-22 00:00:00

  • Click chemistry and bioorthogonal reactions: unprecedented selectivity in the labeling of biological molecules.

    abstract::In recent years, a number of bioorthogonal reactions have been developed, exemplified by click chemistry, that enable the efficient formation of a specific product, even within a highly complex chemical environment. While the exquisite selectivity and reliability of these transformations have led to their broad applic...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/bi9007726

    authors: Best MD

    更新日期:2009-07-21 00:00:00

  • Analysis of the structural core of the human estrogen receptor ligand binding domain by selective proteolysis/mass spectrometric analysis.

    abstract::The structure of the ca. 250 amino acid hormone binding domain of the human estrogen receptor (hER-LBD), expressed in E. coli and purified as a complex with estradiol, has been probed by selective proteolysis, with analysis of the protein fragments both by classical methods (SDS-PAGE and Edman N-terminal sequencing) a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00039a016

    authors: Seielstad DA,Carlson KE,Kushner PJ,Greene GL,Katzenellenbogen JA

    更新日期:1995-10-03 00:00:00

  • Enzymatic assembly of epothilones: the EpoC subunit and reconstitution of the EpoA-ACP/B/C polyketide and nonribosomal peptide interfaces.

    abstract::The biosynthesis of epothilones, a family of hybrid polyketide (PK)/nonribosomal peptide (NRP) antitumor agents, provides an ideal system to study a hybrid PK/NRP natural product with significant biomedical value. Here the third enzyme involved in epothilone production, the five domain 195 kDa polyketide synthase (PKS...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi020006w

    authors: O'Connor SE,Chen H,Walsh CT

    更新日期:2002-04-30 00:00:00

  • Aromatic C-methyltransferases with antipodal stereoselectivity for structurally diverse phenolic amino acids catalyze the methylation step in the biosynthesis of the actinomycin chromophore.

    abstract::The actinomycin biosynthetic gene cluster of Streptomyces chrysomallus harbors two paralogous genes, acmI and acmL, encoding methyltransferases. To unveil their suspected role in the formation of 3-hydroxy-4-methyl-anthranilic acid (4-MHA), the building block of the actinomycin chromophore, each gene was expressed in ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi101422r

    authors: Crnovcić I,Süssmuth R,Keller U

    更新日期:2010-11-16 00:00:00

  • Characterization of the carboxylate delivery module of transcarboxylase: following spontaneous decarboxylation of the 1.3S-CO2- subunit by NMR and FTIR spectroscopies.

    abstract::Transcarboxylase (TC) is a multisubunit enzyme that catalyzes the transfer of a carboxylate group from methylmalonyl-CoA (MMCoA) to pyruvate. The CO2- group is shuttled between the MMCoA and pyruvate binding sites by a biotin cofactor, covalently linked to the 1.3S subunit. Fully carboxylated 1.3S can be prepared in v...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0116442

    authors: Rivera-Hainaj RE,Pusztai-Carey M,Venkat Reddy D,Choowongkomon K,Sönnichsen FD,Carey PR

    更新日期:2002-02-19 00:00:00

  • Intramolecular dephosphorylation of ERK by MKP3.

    abstract::The dual specificity mitogen-activated protein kinase phosphatase MKP3 downregulates mitogenic signaling through dephosphorylation of extracellular signal-regulated kinase (ERK). Like other MKPs, MKP3 consists of a noncatalytic N-terminal domain and a catalytic C-terminal domain. ERK binding to the N-terminal noncatal...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi035346b

    authors: Kim Y,Rice AE,Denu JM

    更新日期:2003-12-30 00:00:00

  • Enzymatic activation of DNA cleavage by dynemicin A and synthetic analogs.

    abstract::Dynemicin A (1), a member of the enediyne family of natural products, binds to double-stranded DNA (K(B) approximately 10(4) M(-1)) and in the presence of millimolar concentrations of a reducing cofactor such as NADPH or GSH reacts to cleave DNA. In this work, we show that the two flavin-based enzymes ferredoxin-NADP+...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi962976n

    authors: Myers AG,Kort ME,Cohen SB,Tom NJ

    更新日期:1997-04-01 00:00:00

  • Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities.

    abstract::Seven hydrophobic residues ranging in size from glycine to phenylalanine have been substituted for the wild-type methionine residue at position 13 in a 15-residue truncated version (S15) of S-peptide, the small component of ribonuclease S. Complexes of both S-15 and the seven variants with S-protein yielded isomorphou...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00164a005

    authors: Varadarajan R,Richards FM

    更新日期:1992-12-15 00:00:00

  • Identification of a lipolysis-stimulated receptor that is distinct from the LDL receptor and the LDL receptor-related protein.

    abstract::This paper provides further characterization of a receptor that, in cells lacking the LDL receptor (FH fibroblasts), mediates lipoprotein binding, uptake, and degradation when incubated with oleate at concentrations not exceeding albumin binding capacity. This oleate-activated receptor is genetically distinct from the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00171a017

    authors: Yen FT,Mann CJ,Guermani LM,Hannouche NF,Hubert N,Hornick CA,Bordeau VN,Agnani G,Bihain BE

    更新日期:1994-02-08 00:00:00

  • Chemical modification of the bovine mitochondrial bc1 complex reveals critical acidic residues involved in the proton pumping activity.

    abstract::Bovine heart ubiquinol-cytochrome c reductase (bc1 complex) was modified with N-(ethoxycarbonyl)-2-ethoxy-1,2-dihydroquinoline (EEDQ), which is a selective reagent for buried carboxyl groups. EEDQ treatment caused a loss of the proton pumping activity of liposome-reconstituted bc1 complex, without effect on the passiv...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9724164

    authors: Cocco T,Di Paola M,Papa S,Lorusso M

    更新日期:1998-02-17 00:00:00

  • Characterization of electron tunneling and hole hopping reactions between different forms of MauG and methylamine dehydrogenase within a natural protein complex.

    abstract::Respiration, photosynthesis, and metabolism require the transfer of electrons through and between proteins over relatively long distances. It is critical that this electron transfer (ET) occur with specificity to avoid cellular damage, and at a rate that is sufficient to support the biological activity. A multistep ho...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi300817d

    authors: Choi M,Shin S,Davidson VL

    更新日期:2012-09-04 00:00:00

  • Spectroscopic Investigation of Cysteamine Dioxygenase.

    abstract::Thiol dioxygenases are mononuclear non-heme FeII-dependent metalloenzymes that initiate the oxidative catabolism of thiol-containing substrates to their respective sulfinates. Cysteine dioxygenase (CDO), the best characterized mammalian thiol dioxygenase, contains a three-histidine (3-His) coordination environment rat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.0c00267

    authors: Fernandez RL,Dillon SL,Stipanuk MH,Fox BG,Brunold TC

    更新日期:2020-07-07 00:00:00

  • Effect of an Ala81His mutation on the Met80 loop dynamics of iso-1-cytochrome c.

    abstract::An A81H variant of yeast iso-1-cytochrome c is prepared to test the hypothesis that the steric size of the amino acid at sequence position 81 of cytochrome c, which has evolved from Ala in yeast to Ile in mammals, slows the dynamics of the opening of the heme crevice. The A81H mutation is used both to increase steric ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi501252z

    authors: Bandi S,Bowler BE

    更新日期:2015-03-10 00:00:00

  • Reactivity of essential thiols of myosin. Chemical probes of the activated state.

    abstract::14C-Labeled fluorodinitrobenzene and N-ethylmaleimide have been used as chemical probes of the conformational states of myosin induced by the binding of MgADP and MgATP. The results indicate that in the high-energy conformation, MMgADP-Pi, the essential thiols are protected from modification but their diminished react...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00643a005

    authors: Reisler E,Burke M,Harrington WF

    更新日期:1977-11-29 00:00:00

  • Carbon-13 nuclear magnetic resonance studies on the interaction of glycophorin with lecithin in reconstituted vesicles.

    abstract::Glycophorin, the MN blood group substance, is a major intrinsic glycoprotein in erythrocyte membranes. The interaction of glycophorin with phosphatidylcholine, 13C-labeled in specific positions in reconstituted unilamellar vesicles, was investigated by using the 13C NMR technique. 1-Palmitoyl-2-([14-13C]linoleoyl)-sn-...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00552a016

    authors: Utsumi H,Tunggal BD,Stoffel W

    更新日期:1980-05-27 00:00:00

  • Structural analysis of integrin recognition and the inhibition of integrin-mediated cell functions by novel nonpeptidic surrogates of the Arg-Gly-Asp sequence.

    abstract::The pivotal role of the Arg-Gly-Asp (RGD) peptide motif in integrin-mediated cell adhesive interactions with extracellular matrix and plasma proteins stimulated the present design of nonpeptidic mimetics of this sequence. To probe the structural requirements for RGD recognition by integrins, we designed various struct...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00055a002

    authors: Greenspoon N,Hershkoviz R,Alon R,Varon D,Shenkman B,Marx G,Federman S,Kapustina G,Lider O

    更新日期:1993-02-02 00:00:00

  • Conformation as the determinant of saccharide binding in concanavalin A: Ca2+-concanavalin A complexes.

    abstract::The existence of two conformational states of concanavalin A (Con A) with different metal ion binding properties has been recently demonstrated (Brown, R. D., Brewer, C. F., & Koenig, S. H. (1977) Biochemistry 16, 3883). Introduction of Mn2+ to the S1 site and Ca2+ to the S2 site of apo-Con A was shown to induce a con...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00613a022

    authors: Koenig SH,Brewer CF,Brown RD 3rd

    更新日期:1978-10-03 00:00:00

  • Peptide models of protein folding initiation sites. 2. The G-H turn region of myoglobin acts as a helix stop signal.

    abstract::A series of peptide fragments of sperm whale myoglobin, corresponding to segments of the region between the G- and H-helices of the protein, have been synthesized and their conformational preferences investigated using circular dichroism and nuclear magnetic resonance spectroscopy in aqueous solution and in solvent mi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00076a007

    authors: Shin HC,Merutka G,Waltho JP,Wright PE,Dyson HJ

    更新日期:1993-06-29 00:00:00

  • Role of enzyme-peptide substrate backbone hydrogen bonding in determining protein kinase substrate specificities.

    abstract::As part of a search for peptides that have specificity for selected protein kinases, the possibility that adenosine cyclic 3',5'-phosphate dependent protein kinase (A-kinase) recognizes the hydrogen-bonding potential of its peptide substrates was investigated. A-Kinase catalyzes the phosphorylation of five N alpha-met...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00388a041

    authors: Thomas NE,Bramson HN,Miller WT,Kaiser ET

    更新日期:1987-07-14 00:00:00

  • Mechanism of flavin reduction in class 2 dihydroorotate dehydrogenases.

    abstract::Dihydroorotate dehydrogenases (DHODs) oxidize dihydroorotate (DHO) to orotate using the FMN prosthetic group to abstract a hydride equivalent from C6 and a protein residue (Ser for Class 2 DHODs) to deprotonate C5. The fundamental question of whether the scission of the two DHO C-H bonds is concerted or stepwise was a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi060919g

    authors: Fagan RL,Nelson MN,Pagano PM,Palfey BA

    更新日期:2006-12-19 00:00:00