Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductases.

Abstract:

:The major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria gonorrhoeae is essential for cell growth under oxygen limiting conditions in the presence of nitrite and is protective against killing by human sera. A phylogenic analysis indicates that AniA is a member of a new class of copper-containing nitrite reductases. Expression of the soluble domain of AniA yields a protein capable of reducing nitrite with specific activity of 160 units/mg, approximately 50 % of that measured for the nitrite reductase from the strong soil denitrifier Alcaligenes faecalis S-6. The crystal structure of the soluble domain of AniA was solved by molecular replacement and sixfold averaging to a resolution of 2.4 A. The nitrite soaked AniA crystal structure refined to 1.95 A reveals a bidentate mode of substrate binding to the type II copper. Despite low sequence identity (approximately 30 %), the core cupredoxin fold of AniA is similar to that found in copper-containing nitrite reductases from soil bacteria. The main structural differences are localized to two attenuated surface loops that map to deletions in the sequence alignment. In soil nitrite reductases, one of these surface loops is positioned near the type I copper site and contributes residues to the docking surface for proteaceous electron donors. In AniA, the attenuation of this loop results in a restructured hydrophobic binding surface that may be required to interact with a lipid anchored azurin. The second attenuated loop is positioned on the opposite side of AniA and may facilitate a more intimate interaction with the lipid membrane. A unique combination of structural effectors surrounding the type I copper site of sAnia contribute to a unusual visible absorption spectra with components observed previously in either green or blue type I copper sites.

journal_name

J Mol Biol

authors

Boulanger MJ,Murphy ME

doi

10.1006/jmbi.2001.5251

keywords:

subject

Has Abstract

pub_date

2002-02-01 00:00:00

pages

1111-27

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022283601952519

journal_volume

315

pub_type

杂志文章
  • Structural assembly of the active site in an aldo-keto reductase by NADPH cofactor.

    abstract::A 1.9 A resolution X-ray structure of the apo-form of Corynebacterium 2,5-diketo-d-gluconic acid reductase A (2,5-DKGR A), a member of the aldo-keto reductase superfamily, has been determined by molecular replacement using the NADPH-bound form of the same enzyme as the search model. 2,5-DKGR A catalyzes the NADPH-depe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4739

    authors: Sanli G,Blaber M

    更新日期:2001-06-22 00:00:00

  • Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system.

    abstract::Bacteriophage capsid assembly pathways provide excellent model systems to study large-scale conformational changes and other mechanisms that regulate the formation of macromolecular complexes. These capsids are formed from proheads: relatively fragile precursor particles which mature by undergoing extensive remodeling...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0538

    authors: Conway JF,Duda RL,Cheng N,Hendrix RW,Steven AC

    更新日期:1995-10-13 00:00:00

  • Exploring the regulation of tRNA distribution on the genomic scale.

    abstract::Though up to 20% of the total RNA in bacterial cells is tRNA, the regulation of tRNA distribution on the genomic level remains unclear. tRNA distribution is governed by four processes: transcription, processing of precursor tRNA, degradation of precursor tRNA and degradation of mature tRNA. To elucidate the relationsh...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.01.024

    authors: Dittmar KA,Mobley EM,Radek AJ,Pan T

    更新日期:2004-03-12 00:00:00

  • Use of binding site neighbor-effect parameters to evaluate the interactions between adjacent ligands on a linear lattice. Effects on ligand-lattice association.

    abstract::A method using binding site "neighbor-effect" parameters (NEPs) is introduced to evaluate the effects of interaction between adjacent ligands on their binding to an infinite linear lattice. Binding site overlap is also taken into account. This enables the conditional probability approach of McGhee & von Hippel to be e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90262-i

    authors: Wolfe AR,Meehan T

    更新日期:1992-02-20 00:00:00

  • Conservation of transition state structure in fast folding peripheral subunit-binding domains.

    abstract::Phi-value analysis was used to characterise the structure of the transition state (TS) for folding of POB L146A Y166W, a peripheral subunit-binding domain that folds in microseconds. Helix 2 was structured in the TS with consolidating interactions from the structured loop that connects the two alpha-helices. This dist...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.06.081

    authors: Sharpe TD,Ferguson N,Johnson CM,Fersht AR

    更新日期:2008-10-31 00:00:00

  • Detection of single-stranded DNA in scrapie-infected brain by electron microscopy.

    abstract::The nucleic acid content of enriched preparations of mitochondria/tubulofilamentous particles from normal and scrapie-infected hamster brains were examined by electron microscopy. After spreading on collodion-coated grids circular molecules of approximately 15.7 kb corresponding in size to mitochondrial DNA (mtDNA) we...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90369-W

    authors: Narang HK

    更新日期:1990-12-05 00:00:00

  • Effects of neutral salts on RNA chain elongation and pausing by Escherichia coli RNA polymerase.

    abstract::We examined the effects of neutral salts and the non-ionic solute 2-methyl,-2,4-pentanediol (MPD) on transcript elongation by Escherichia coli RNA polymerase and on pausing induced by the multipartite his leader pause signal. All solutes tested slowed the overall rate of elongation, with anions showing the dominant ef...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0934

    authors: Chan CL,Landick R

    更新日期:1997-04-25 00:00:00

  • Protein titration in the crystal state.

    abstract::Proteins are complex structures whose overall stability critically depends on a delicate balance of numerous interactions of similar strength, which are markedly influenced by their environment. Here, we present an analysis of the effect of pH on a protein structure in the crystalline state using RNase A as a model sy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3093

    authors: Berisio R,Lamzin VS,Sica F,Wilson KS,Zagari A,Mazzarella L

    更新日期:1999-10-01 00:00:00

  • What drives proteins into the major or minor grooves of DNA?

    abstract::The energetic profiles of a significant number of protein-DNA systems at 20 degrees C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy-driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by fa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2006.09.059

    authors: Privalov PL,Dragan AI,Crane-Robinson C,Breslauer KJ,Remeta DP,Minetti CA

    更新日期:2007-01-05 00:00:00

  • A structural model for the DEAD box helicase YxiN in solution: localization of the RNA binding domain.

    abstract::DEAD box proteins consist of a common helicase core formed by two globular RecA domains that are separated by a cleft. The helicase core acts as a nucleotide-dependent switch that alternates between open and closed conformations during the catalytic cycle of duplex separation, thereby providing basic helicase activity...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.07.049

    authors: Karow AR,Klostermeier D

    更新日期:2010-10-01 00:00:00

  • Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes.

    abstract::Nonstandard nucleotide triphosphate pyrophosphatase (NTPase) can efficiently hydrolyze nonstandard purine nucleotides in the presence of divalent cations. The crystal structures of the NTPase from Pyrococcus horikoshii OT3 (PhNTPase) have been determined in two unliganded forms and in three liganded forms with inosine...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.11.018

    authors: Lokanath NK,Pampa KJ,Takio K,Kunishima N

    更新日期:2008-01-25 00:00:00

  • DNA cleavage at two recognition sites by the SfiI restriction endonuclease: salt dependence of cis and trans interactions between distant DNA sites.

    abstract::At low ionic strength, the SfiI restriction enzyme cleaved at similar rates both supercoiled and linear DNA with two SfiI sites and linear DNA with one SfiI site. For the substrates with two sites, the majority of the DNA was converted directly to products cut at both sites; the enzyme appears to bind to two sites bef...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0506

    authors: Nobbs TJ,Halford SE

    更新日期:1995-09-29 00:00:00

  • The mechanical role of VASP in an Arp2/3-complex-based motility assay.

    abstract::The comet motility assay, inspired by Listeria locomotion, has been used extensively as an in vitro model to study the structural and motile properties of the actin cytoskeleton. However, there are no quantitative measurements of the mechanical properties of these actin comets. In this work, we use nanoindentation bas...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.08.054

    authors: Suei S,Seyan R,Noguera P,Manzi J,Plastino J,Kreplak L

    更新日期:2011-10-28 00:00:00

  • Subdomain competition, cooperativity, and topological frustration in the folding of CheY.

    abstract::The folding of multidomain proteins often proceeds in a hierarchical fashion with individual domains folding independent of one another. A large single-domain protein, however, can consist of multiple modules whose folding may be autonomous or interdependent in ways that are unclear. We used coarse-grained simulations...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.07.007

    authors: Hills RD Jr,Brooks CL 3rd

    更新日期:2008-10-03 00:00:00

  • Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH.

    abstract::Foot-and-mouth disease virus (FMDV), a non-enveloped picornavirus, is sensitive to acidic conditions. At pH values below 7 the icosahedral virus capsid, formed from 60 copies of a protomer containing four polypeptides (VP1 to 4), dissociates into 12 pentamers, releasing the viral RNA. Evidence suggests that this acid ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1418

    authors: van Vlijmen HW,Curry S,Schaefer M,Karplus M

    更新日期:1998-01-16 00:00:00

  • Contributions of Histone Variants in Nucleosome Structure and Function.

    abstract::Chromatin compacts genomic DNA in eukaryotes. The primary chromatin unit is the nucleosome core particle, composed of four pairs of the core histones, H2A, H2B, H3, and H4, and 145-147 base pairs of DNA. Since replication, recombination, repair, and transcription take place in chromatin, the structure and dynamics of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2020.10.012

    authors: Kurumizaka H,Kujirai T,Takizawa Y

    更新日期:2020-10-14 00:00:00

  • Very fast folding and association of a trimerization domain from bacteriophage T4 fibritin.

    abstract::The foldon domain constitutes the C-terminal 30 amino acid residues of the trimeric protein fibritin from bacteriophage T4. Its function is to promote folding and trimerization of fibritin. We investigated structure, stability and folding mechanism of the isolated foldon domain. The domain folds into the same trimeric...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.02.020

    authors: Güthe S,Kapinos L,Möglich A,Meier S,Grzesiek S,Kiefhaber T

    更新日期:2004-04-02 00:00:00

  • Molecular model of an alpha-helical prion protein dimer and its monomeric subunits as derived from chemical cross-linking and molecular modeling calculations.

    abstract::Prions are the agents of a series of lethal neurodegenerative diseases. They are composed largely, if not entirely, of the host-encoded prion protein (PrP), which can exist in the cellular isoform PrP(C) and the pathological isoform PrP(Sc). The conformational change of the alpha-helical PrP(C) into beta-sheet-rich Pr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.11.035

    authors: Kaimann T,Metzger S,Kuhlmann K,Brandt B,Birkmann E,Höltje HD,Riesner D

    更新日期:2008-02-15 00:00:00

  • DNA target site requirements for homing in vivo of a bacterial group II intron encoding a protein lacking the DNA endonuclease domain.

    abstract::Group II intron-encoded proteins (IEPs), which have maturase and reverse transcriptase activities, form a ribonucleoprotein (RNP) complex with the intron RNA. Some IEPs also have a C-terminal DNA-binding region and conserved DNA endonuclease domain involved in the recognition and cleavage of specific DNA target sites ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01380-3

    authors: Jiménez-Zurdo JI,García-Rodríguez FM,Barrientos-Durán A,Toro N

    更新日期:2003-02-14 00:00:00

  • Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data.

    abstract::X-ray crystallography and NMR can provide detailed structural information of protein-protein complexes, but technical problems make their application challenging in the high-throughput regime. Other methods such as small-angle X-ray scattering (SAXS) are more promising for large-scale application, but at the cost of l...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.08.029

    authors: Pons C,D'Abramo M,Svergun DI,Orozco M,Bernadó P,Fernández-Recio J

    更新日期:2010-10-22 00:00:00

  • The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products.

    abstract::Precise regulation of dNTPs within the cellular nucleotide pool is essential for high accuracy of DNA replication and is critical for retaining the genomic integrity. Recently, human dCTPase (deoxycytidine triphosphatase), also known as DCTPP1 (human all-alpha dCTP pyrophosphatase 1), has been revealed to be a key pla...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.01.005

    authors: Scaletti E,Claesson M,Helleday T,Jemth AS,Stenmark P

    更新日期:2020-02-14 00:00:00

  • Conformational changes of a viral capsid protein. Thermodynamic rationale for proteolytic regulation of bacteriophage T4 capsid expansion, co-operativity, and super-stabilization by soc binding.

    abstract::We have used differential scanning calorimetry in conjunction with cryo-electron microscopy to investigate the conformational transitions undergone by the maturing capsid of phage T4. Its precursor shell is composed primarily of gp23 (521 residues): cleavage of gp23 to gp23* (residues 66 to 521) facilitates a concerte...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90871-g

    authors: Steven AC,Greenstone HL,Booy FP,Black LW,Ross PD

    更新日期:1992-12-05 00:00:00

  • A genetic analysis of crystal growth.

    abstract::The regulation of crystal morphology by proteins is often observed in biology. It is a central feature in the formation of hard tissues such as bones, teeth and mollusc shells. We have developed a genetic system in the bacterium Escherichia coli to study the protein-mediated control of crystal growth. We have used the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3682

    authors: Brown S,Sarikaya M,Johnson E

    更新日期:2000-06-09 00:00:00

  • Kinetic and structural characterisation of Escherichia coli nitroreductase mutants showing improved efficacy for the prodrug substrate CB1954.

    abstract::Escherichia coli nitroreductase (NTR) is a flavoprotein that reduces a variety of quinone and nitroaromatic substrates. Among these substrates is the prodrug 5-[aziridin-1-yl]-2,4-dinitrobenzamide (CB1954) that is activated by NTR to form two products, one of which is highly cytotoxic. NTR in combination with CB1954 h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.02.012

    authors: Race PR,Lovering AL,White SA,Grove JI,Searle PF,Wrighton CW,Hyde EI

    更新日期:2007-04-27 00:00:00

  • Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus.

    abstract::Although multiple viruses utilize host cell cyclophilins, including severe acute respiratory syndrome (SARS) and human immunodeficiency virus type-1(HIV-1), their role in infection is poorly understood. To help elucidate these roles, we have characterized the first virally encoded cyclophilin (mimicyp) derived from th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.08.051

    authors: Thai V,Renesto P,Fowler CA,Brown DJ,Davis T,Gu W,Pollock DD,Kern D,Raoult D,Eisenmesser EZ

    更新日期:2008-04-18 00:00:00

  • Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid.

    abstract::We demonstrate, using transmission electron microscopy and immunopurification with an antibody specific for RNA/DNA hybrid, that intact mitochondrial DNA replication intermediates are essentially duplex throughout their length but contain extensive RNA tracts on one strand. However, the extent of preservation of RNA i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.02.029

    authors: Pohjoismäki JL,Holmes JB,Wood SR,Yang MY,Yasukawa T,Reyes A,Bailey LJ,Cluett TJ,Goffart S,Willcox S,Rigby RE,Jackson AP,Spelbrink JN,Griffith JD,Crouch RJ,Jacobs HT,Holt IJ

    更新日期:2010-04-16 00:00:00

  • Engineering activity and stability of Thermotoga maritima glutamate dehydrogenase. II: construction of a 16-residue ion-pair network at the subunit interface.

    abstract::The role of an 18-residue ion-pair network, that is present in the glutamate dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus, in conferring stability to other, less stable homologous enzymes, has been studied by introducing four new charged amino acid residues into the subunit interface of glutam...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2779

    authors: Lebbink JH,Knapp S,van der Oost J,Rice D,Ladenstein R,de Vos WM

    更新日期:1999-06-04 00:00:00

  • Regulation of mating-type information in yeast. Negative control requiring sequences both 5' and 3' to the regulated region.

    abstract::The genome of the yeast Saccharomyces cerevisiae contains three complete copies of the genetic information governing cell mating type. Normally, only the information in one of the copies (the MAT locus) is expressed; the other two copies (HML and HMR) are repressed and serve as donors of mating-type sequences that can...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90492-3

    authors: Abraham J,Nasmyth KA,Strathern JN,Klar AJ,Hicks JB

    更新日期:1984-07-05 00:00:00

  • Different intrastrand and interstrand contributions to stacking account for roll variations at the alternating purine-pyrimidine sequences in A-DNA and A-RNA.

    abstract::An explanation is suggested for the roll alternation between low and high values in A-type nucleic acid duplexes containing alternating sequences of purine and pyrimidine residues. The explanation combines two points. (1) Roll inevitably occurs in A-type duplexes due to geometrical reasons. (2) Intrastrand base stacki...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)80172-q

    authors: Sponer J,Kypr J

    更新日期:1991-10-05 00:00:00

  • The high-affinity interaction of human IL-4 and the receptor alpha chain is constituted by two independent binding clusters.

    abstract::IL4-BP, the extracellular binding domain of the IL-4 receptor alpha chain, contains a high-affinity binding epitope for IL-4 (K(D) 150 pM). Previous results on the crystal structure of the IL-4/IL4-BP complex and on the functional epitope of IL-4 suggested that this contact comprises a mosaic of two binding clusters. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5243

    authors: Zhang JL,Simeonowa I,Wang Y,Sebald W

    更新日期:2002-01-18 00:00:00