Function of His185 in Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase.

Abstract:

:Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) catalyzes the condensation of arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) by favoring the activation of a water molecule coordinated to the active-site metal ion. Cys11, His185, Glu222 and Asp233 are the other metal ligands. Wild-type KDO8PS is purified with Zn(2+) or Fe(2+) in the active site, but maximal activity in vitro is achieved when the endogenous metal is replaced with Cd(2+). The H185G enzyme retains 8% of the wild-type activity. ICP mass spectrometry analysis indicates that loss of His185 decreases the enzyme affinity for Fe(2+), but not for Zn(2+). However, maximal activity is again achieved by substitution of the endogenous metal with Cd(2+). We have determined the X-ray structures of the Cd(2+) H185G enzyme in its substrate-free form, and in complex with PEP, and PEP plus A5P. These structures show a normal amount of Cd(2+) bound, suggesting that coordination by His185 is not essential to retain Cd(2+) in the active site. Nonetheless, there are significant changes in the coordination sphere of Cd(2+) with respect to the wild-type enzyme, as the carboxylate moiety of PEP binds directly to the metal ion and replaces water and His185 as ligands. These observations indicate that the primary function of His185 in A.aeolicus KDO8PS is to orient PEP in the active site of the enzyme in such a way that a water molecule on the sinister (si) side of PEP can be activated by direct coordination to the metal ion.

journal_name

J Mol Biol

authors

Wang J,Duewel HS,Stuckey JA,Woodard RW,Gatti DL

doi

10.1016/s0022-2836(02)01096-3

keywords:

subject

Has Abstract

pub_date

2002-11-22 00:00:00

pages

205-14

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022283602010963

journal_volume

324

pub_type

杂志文章
  • The malignant brain tumor repeats of human SCML2 bind to peptides containing monomethylated lysine.

    abstract::SCML2 (sex comb on midleg-like 2) is a constituent of the Polycomb repressive complex 1, a large multiprotein assembly required for the repression of developmental control genes. It contains two MBT (malignant brain tumor) repeats; the MBT is a protein module structurally similar to domains that bind to methylated his...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.07.081

    authors: Santiveri CM,Lechtenberg BC,Allen MD,Sathyamurthy A,Jaulent AM,Freund SM,Bycroft M

    更新日期:2008-10-24 00:00:00

  • Determination of the MurD mechanism through crystallographic analysis of enzyme complexes.

    abstract::UDP -N- acetylmuramoyl- L -alanine: D -glutamate (MurD) ligase catalyses the addition of d -glutamate to the nucleotide precursor UDP -N- acetylmuramoyl- L -alanine (UMA). The crystal structures of three complexes of Escherichia coli MurD with a variety of substrates and products have been determined to high resolutio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2800

    authors: Bertrand JA,Auger G,Martin L,Fanchon E,Blanot D,Le Beller D,van Heijenoort J,Dideberg O

    更新日期:1999-06-11 00:00:00

  • The replisome organizer (G38P) of Bacillus subtilis bacteriophage SPP1 forms specialized nucleoprotein complexes with two discrete distant regions of the SPP1 genome.

    abstract::Initiation of Bacillus subtilis bacteriophage SPP1 DNA replication requires the products of genes 38, 39 and 40 (G38P, G39P and G40P). G38P specifically binds two discrete regions, which are 32.1 kb apart in a linear map of the SPP1 genome. One of these target sites, which maps at the left end of the phage genome, wit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1060

    authors: Missich R,Weise F,Chai S,Lurz R,Pedré X,Alonso JC

    更新日期:1997-07-04 00:00:00

  • Specific tyrosylation of the bulky tRNA-like structure of brome mosaic virus RNA relies solely on identity nucleotides present in its amino acid-accepting domain.

    abstract::Residues specifying aminoacylation by yeast tyrosyl-tRNA synthetase (TyrRS) of the tRNA-like structure present at the 3'-end of brome mosaic virus (BMV) RNA were determined by the in vitro approach using phage T7 transcripts. They correspond to nucleotides equivalent to base-pair C1-G72 and discriminator base A73 in t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4654

    authors: Fechter P,Giegé R,Rudinger-Thirion J

    更新日期:2001-06-01 00:00:00

  • Crystallization of catechol-1,2 dioxygenase from Pseudomonas arvilla C-1.

    abstract::The metalloenzyme catechol 1,2-dioxygenase from Pseudomonas arvilla C-1 consists of three isozymes formed by combinations of two non-identical subunits; alpha alpha, alpha beta and beta beta; with molecular masses of 59,000, 63,000 and 67,000 Da, respectively. The alpha alpha isozyme crystallizes in the orthorhombic s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1144

    authors: Earhart CA,Hall MD,Michaud-Soret I,Que L Jr,Ohlendorf DH

    更新日期:1994-02-11 00:00:00

  • Sixteen discrete RNA components in the cytoplasmic ribosome of Euglena gracilis.

    abstract::We have isolated cytoplasmic ribosomes from Euglena gracilis and characterized the RNA components of these particles. We show here that instead of the four rRNAs (17-19 S, 25-28 S, 5.8 S and 5 S) found in typical eukaryotic ribosomes, Euglena cytoplasmic ribosomes contain 16 RNA components. Three of these Euglena rRNA...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(05)80096-8

    authors: Schnare MN,Gray MW

    更新日期:1990-09-05 00:00:00

  • Structure of a Ca(2+)/CaM:Kv7.4 (KCNQ4) B-helix complex provides insight into M current modulation.

    abstract::Calmodulin (CaM) is an important regulator of Kv7.x (KCNQx) voltage-gated potassium channels. Channels from this family produce neuronal M currents and cardiac and auditory I(KS) currents and harbor mutations that cause arrhythmias, epilepsy, and deafness. Despite extensive functional characterization, biochemical and...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.11.023

    authors: Xu Q,Chang A,Tolia A,Minor DL Jr

    更新日期:2013-01-23 00:00:00

  • The MCM Helicase Motor of the Eukaryotic Replisome.

    abstract::The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2016.01.024

    authors: Abid Ali F,Costa A

    更新日期:2016-05-08 00:00:00

  • Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern.

    abstract::Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex. Structure-activity relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding spec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.05.053

    authors: Huang LS,Cobessi D,Tung EY,Berry EA

    更新日期:2005-08-19 00:00:00

  • Translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining.

    abstract::Ribosomal subunit joining is a key checkpoint in the bacterial translation initiation pathway during which initiation factors (IFs) regulate association of the 30S initiation complex (IC) with the 50S subunit to control formation of a 70S IC that can enter into the elongation stage of protein synthesis. The GTP-bound ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.09.024

    authors: MacDougall DD,Gonzalez RL Jr

    更新日期:2015-05-08 00:00:00

  • Comparison of the human apolipoprotein genes. Apo AII presents a unique functional intron-exon junction.

    abstract::The structure and function of the apolipoproteins are of interest because of their central role in lipid metabolism. We report the complete primary structure of the human apo AII and CIII genes. These, like apo AI, contain three introns located at conserved positions. This may reflect their evolutionary and functional...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90255-4

    authors: Shelley CS,Sharpe CR,Baralle FE,Shoulders CC

    更新日期:1985-11-05 00:00:00

  • A 50th order reaction predicted and observed for sickle hemoglobin nucleation.

    abstract::Sickle hemoglobin polymerization exhibits a striking sensitivity to initial concentration, with characteristic reaction times that exhibit 30th power dependence on concentration. This extraordinary reaction order is encompassed by a novel double nucleation mechanism that predicts 50th power dependence of the homogeneo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0079

    authors: Cao Z,Ferrone FA

    更新日期:1996-02-23 00:00:00

  • Specific RNA-binding antibodies with a four-amino-acid code.

    abstract::Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.03.003

    authors: Sherman EM,Holmes S,Ye JD

    更新日期:2014-05-15 00:00:00

  • How thioredoxin can reduce a buried disulphide bond.

    abstract::We present a study of the interaction between thioredoxin and the model enzyme pI258 arsenate reductase (ArsC) from Staphylococcus aureus. ArsC catalyses the reduction of arsenate to arsenite. Three redox active cysteine residues (Cys10, Cys82 and Cys89) are involved. After a single catalytic arsenate reduction event,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.04.016

    authors: Messens J,Van Molle I,Vanhaesebrouck P,Limbourg M,Van Belle K,Wahni K,Martins JC,Loris R,Wyns L

    更新日期:2004-06-04 00:00:00

  • Mutations in beta-myosin S2 that cause familial hypertrophic cardiomyopathy (FHC) abolish the interaction with the regulatory domain of myosin-binding protein-C.

    abstract::The myosin filaments of striated muscle contain a family of enigmatic myosin-binding proteins (MyBP), MyBP-C and MyBP-H. These modular proteins of the intracellular immunoglobulin superfamily contain unique domains near their N termini. The N-terminal domain of cardiac MyBP-C, the MyBP-C motif, contains additional pho...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2522

    authors: Gruen M,Gautel M

    更新日期:1999-02-26 00:00:00

  • Growth of sea cucumber collagen fibrils occurs at the tips and centers in a coordinated manner.

    abstract::Collagen fibrils are the principle source of mechanical strength in the mutable dermis of the sea cucumber Cucumaria frondosa. To obtain information about the mechanism by which collagen molecules self-assemble into fibrils, we have isolated single intact fibrils with lengths in the range 14-444 microm. These fibrils ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2230

    authors: Trotter JA,Chapman JA,Kadler KE,Holmes DF

    更新日期:1998-12-18 00:00:00

  • Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending.

    abstract::Monovalent cation binding sites on nucleic acids in solution can be localized using the isotopically labeled ammonium ion (15NH4+) as a probe in high resolution NMR spectroscopy experiments. The application of this technique to a series of DNA duplexes reveals a preference for the binding of ammonium cations in the mi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2513

    authors: Hud NV,Sklenár V,Feigon J

    更新日期:1999-02-26 00:00:00

  • Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae.

    abstract::There are at least three different kinds of short interspersed repetitive elements in salmonid genomes. Of these, members of the HpaI family are found to be most widely distributed in salmonid species. The HpaI family is present with high copy numbers in all members of the subfamily Salmoninae, such as salmon, trout a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1540

    authors: Kido Y,Himberg M,Takasaki N,Okada N

    更新日期:1994-09-02 00:00:00

  • Missense mutations in the Bacillus subtilis gnt repressor that diminish operator binding ability.

    abstract::The Bacillus subtilis gnt operon is negatively regulated by the gnt repressor (GntR, 243 amino acids), which is antagonized by gluconate. The GntR protein belongs to a new family of bacterial regulatory proteins (GntR family). To locate the DNA-binding domain of the GntR protein, we obtained mutations of this protein,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1270

    authors: Yoshida K,Fujita Y,Sarai A

    更新日期:1993-05-20 00:00:00

  • Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures.

    abstract::The structure of replicating simian virus 40 (SV40) minichromosomes was studied by DNA crosslinking with trimethyl-psoralen. The procedure was used both in vitro with extracted SV40 minichromosomes as well as in vivo with SV40-infected cells. Both procedures gave essentially the same results. Mature SV40 minichromosom...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90390-6

    authors: Sogo JM,Stahl H,Koller T,Knippers R

    更新日期:1986-05-05 00:00:00

  • Crystal structure of a ternary complex between human prostate-specific antigen, its substrate acyl intermediate and an activating antibody.

    abstract::Human prostate-specific antigen (PSA or KLK3) is an important marker for the diagnosis and management of prostate cancer. This is an androgen-regulated glycoprotein of the kallikrein-related protease family secreted by prostatic epithelial cells. Its physiological function is to cleave semenogelins in the seminal coag...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.11.052

    authors: Ménez R,Michel S,Muller BH,Bossus M,Ducancel F,Jolivet-Reynaud C,Stura EA

    更新日期:2008-02-29 00:00:00

  • Roles for glycosylation of cell surface receptors involved in cellular immune recognition.

    abstract::The majority of cell surface receptors involved in antigen recognition by T cells and in the orchestration of the subsequent cell signalling events are glycoproteins. The length of a typical N-linked sugar is comparable with that of an immunoglobulin domain (30 A). Thus, by virtue of their size alone, oligosaccharides...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1006/jmbi.1999.3104

    authors: Rudd PM,Wormald MR,Stanfield RL,Huang M,Mattsson N,Speir JA,DiGennaro JA,Fetrow JS,Dwek RA,Wilson IA

    更新日期:1999-10-22 00:00:00

  • A conserved element in the yeast RNase MRP RNA subunit can participate in a long-range base-pairing interaction.

    abstract::RNase MRP is a ribonucleoprotein endoribonuclease involved in eukaryotic pre-rRNA processing. The enzyme possesses a putatively catalytic RNA subunit, structurally related to that of RNase P. A thorough structure analysis of Saccharomyces cerevisiae MRP RNA, entailing enzymatic and chemical probing, mutagenesis and th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.05.076

    authors: Walker SC,Avis JM

    更新日期:2004-08-06 00:00:00

  • Archaeal N-terminal protein maturation commonly involves N-terminal acetylation: a large-scale proteomics survey.

    abstract::We present the first large-scale survey of N-terminal protein maturation in archaea based on 873 proteomically identified N-terminal peptides from the two haloarchaea Halobacterium salinarum and Natronomonas pharaonis. The observed protein maturation pattern can be attributed to the combined action of methionine amino...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.07.086

    authors: Falb M,Aivaliotis M,Garcia-Rizo C,Bisle B,Tebbe A,Klein C,Konstantinidis K,Siedler F,Pfeiffer F,Oesterhelt D

    更新日期:2006-10-06 00:00:00

  • The nature of ligand-induced conformational change in transferrin in solution. An investigation using X-ray scattering, XAFS and site-directed mutants.

    abstract::Ligand-induced conformational change in transferrins has been studied by site-directed mutagenesis of human serum half molecule (N-lobe), X-ray absorption fine structure (XAFS) spectroscopy and X-ray solution scattering. Use of recent advances in data analysis has been made for extracting model-independent molecular s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1787

    authors: Grossmann JG,Crawley JB,Strange RW,Patel KJ,Murphy LM,Neu M,Evans RW,Hasnain SS

    更新日期:1998-06-05 00:00:00

  • Mechanism of photosensory adaptation in Halobacterium salinarium.

    abstract::Phototaxis in Halobacterium salinarium is the result of an interplay of sensory rhodopsin excitation and adaptation to the stimulus background. Adaptation to orange light, received by sensory rhodopsin I was probed by measuring the behavioral response of cells to a step-like decrease in intensity. Cells were able to a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.0101

    authors: Marwan W,Bibikov SI,Montrone M,Oesterhelt D

    更新日期:1995-03-03 00:00:00

  • Repression and activation of promoter-bound RNA polymerase activity by Gal repressor.

    abstract::By binding to the DNA site OE at position -60.5 in the gal operon, the GalR protein activates transcription from the P2 promoter located on the opposite face of DNA (position -5) and represses transcription from the P1 promoter located on the same face (position +1). GalR increases RNA polymerase binding at P2 and inh...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1221

    authors: Choy HE,Hanger RR,Aki T,Mahoney M,Murakami K,Ishihama A,Adhya S

    更新日期:1997-09-26 00:00:00

  • Interaction of Alzheimer's A beta peptide with an engineered binding protein--thermodynamics and kinetics of coupled folding-binding.

    abstract::The oligomerization and aggregation of the amyloid-beta (A beta) peptide, a cleavage product of the amyloid precursor protein predominantly 40 or 42 amino acids in length, has been implicated in the pathogenesis of Alzheimer's disease. The identification of A beta-binding agents, e.g., antibodies or peptides, constitu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.02.040

    authors: Hoyer W,Härd T

    更新日期:2008-04-25 00:00:00

  • Combining EPR with fluorescence spectroscopy to monitor conformational changes at the myosin nucleotide pocket.

    abstract::We used spin-labeled nucleotide analogs and fluorescence spectroscopy to monitor conformational changes at the nucleotide-binding site of wild-type Dictyostelium discoideum (WT) myosin and a construct containing a single tryptophan at position F239 near the switch 1 loop. Electron paramagnetic resonance (EPR) spectros...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.12.035

    authors: Naber N,Málnási-Csizmadia A,Purcell TJ,Cooke R,Pate E

    更新日期:2010-03-05 00:00:00

  • Determinants of PB1 Domain Interactions in Auxin Response Factor ARF5 and Repressor IAA17.

    abstract::Auxin is a plant hormone that is central to plant growth and development from embryogenesis to senescence. Auxin signaling is mediated by auxin response transcription factors (ARFs) and Aux/IAA repressors that regulate the expression of a multitude of auxin response genes. ARF and Aux/IAA proteins assemble into homome...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.04.007

    authors: Kim Y,Park C,Cha S,Han M,Ryu KS,Suh JY

    更新日期:2020-06-26 00:00:00