Achromobacter cycloclastes: A species of gram negative, aerobic, denitrifying bacteria in the genus ACHROMOBACTER.Alcaligenes: A genus of gram-negative, aerobic, motile bacteria that occur in water and soil. Some are common inhabitants of the intestinal tract of vertebrates. These bacteria occasionally cause opportunistic infections in humans.Achromobacter: A genus of gram-negative, strictly aerobic, non-spore forming rods. Soil and water are regarded as the natural habitat. They are sometimes isolated from a hospital environment and humans.Nitrite Reductases: A group of enzymes that oxidize diverse nitrogenous substances to yield nitrite. (Enzyme Nomenclature, 1992) EC 1.Achromobacter denitrificans: The type species of gram negative, aerobic bacteria in the genus ACHROMOBACTER. Previously in the genus ALCALIGENES, the classification and nomenclature of this species has been frequently emended. The two subspecies, Achromobacter xylosoxidans subsp. denitrificans and Achromobacter xylosoxidans subsp. xylosoxidans are associated with infections.Azurin: A bacterial protein from Pseudomonas, Bordetella, or Alcaligenes which operates as an electron transfer unit associated with the cytochrome chain. The protein has a molecular weight of approximately 16,000, contains a single copper atom, is intensively blue, and has a fluorescence emission band centered at 308nm.Copper: A heavy metal trace element with the atomic symbol Cu, atomic number 29, and atomic weight 63.55.Phenylpyruvic Acids: A group of compounds that are derivatives of phenylpyruvic acid which has the general formula C6H5CH2COCOOH, and is a metabolite of phenylalanine. (From Dorland, 28th ed)Phenylalanine Ammonia-Lyase: An enzyme that catalyzes the deamination of PHENYLALANINE to form trans-cinnamate and ammonia.Phenylalanine: An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE.Anabaena variabilis: A species of ANABAENA that can form SPORES called akinetes.Phenylalanine Hydroxylase: An enzyme of the oxidoreductase class that catalyzes the formation of L-TYROSINE, dihydrobiopterin, and water from L-PHENYLALANINE, tetrahydrobiopterin, and oxygen. Deficiency of this enzyme may cause PHENYLKETONURIAS and PHENYLKETONURIA, MATERNAL. EC 1.14.16.1.Patents as Topic: Exclusive legal rights or privileges applied to inventions, plants, etc.Transaminases: A subclass of enzymes of the transferase class that catalyze the transfer of an amino group from a donor (generally an amino acid) to an acceptor (generally a 2-keto acid). Most of these enzymes are pyridoxyl phosphate proteins. (Dorland, 28th ed) EC 2.6.1.Pseudomonas aeruginosa: A species of gram-negative, aerobic, rod-shaped bacteria commonly isolated from clinical specimens (wound, burn, and urinary tract infections). It is also found widely distributed in soil and water. P. aeruginosa is a major agent of nosocomial infection.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Pseudomonas Infections: Infections with bacteria of the genus PSEUDOMONAS.Inventions: A novel composition, device, or process, independently conceived de novo or derived from a pre-existing model.Intellectual Property: Property, such as patents, trademarks, and copyright, that results from creative effort. The Patent and Copyright Clause (Art. 1, Sec. 8, cl. 8) of the United States Constitution provides for promoting the progress of science and useful arts by securing for limited times to authors and inventors, the exclusive right to their respective writings and discoveries. (From Black's Law Dictionary, 5th ed, p1014)Hyphomicrobium: A genus of rod-shaped, oval, or bean-shaped bacteria found in soil and fresh water. Polar prosthecae are present and cells reproduce by budding at the tips of the prosthecae. Cells of this genus are aerobic and grow best with one-carbon compounds. (From Bergey's Manual of Determinative Bacteriology, 9th ed)Alcaligenes faecalis: The type species of gram negative bacteria in the genus ALCALIGENES, found in soil. It is non-pathogenic, non-pigmented, and used for the production of amino acids.Nitrites: Salts of nitrous acid or compounds containing the group NO2-. The inorganic nitrites of the type MNO2 (where M=metal) are all insoluble, except the alkali nitrites. The organic nitrites may be isomeric, but not identical with the corresponding nitro compounds. (Grant & Hackh's Chemical Dictionary, 5th ed)Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Nitrite Reductase (NAD(P)H): An enzyme found primarily in BACTERIA and FUNGI that catalyzes the oxidation of ammonium hydroxide to nitrite. It is an iron-sulfur HEME; FLAVOPROTEIN containing siroheme and can utilize both NAD and NADP as cofactors. This enzyme was formerly classified as EC 1.6.6.4.Fatigue: The state of weariness following a period of exertion, mental or physical, characterized by a decreased capacity for work and reduced efficiency to respond to stimuli.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Paracoccus pantotrophus: A species of gram-negative, coccoid, mostly chemolithoautotrophic bacteria, in the family RHODOBACTERACEAE. Some strains can grow anaerobically.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Systems Integration: The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Rhodobacter: A genus of gram-negative bacteria widely distributed in fresh water as well as marine and hypersaline habitats.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Myelin and Lymphocyte-Associated Proteolipid Proteins: A family of MARVEL domain-containing proteolipid proteins involved in vesicular trafficking cycling between the GOLGI COMPLEX and the apical PLASMA MEMBRANE.ItalyFood Inspection: Examination of foods to assure wholesome and clean products free from unsafe microbes or chemical contamination, natural or added deleterious substances, and decomposition during production, processing, packaging, etc.Structure Collapse: Failure in built environment with loss of functional integrity.CholinesterasesColumbidae: Family in the order COLUMBIFORMES, comprised of pigeons or doves. They are BIRDS with short legs, stout bodies, small heads, and slender bills. Some sources call the smaller species doves and the larger pigeons, but the names are interchangeable.Physicians: Individuals licensed to practice medicine.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Lawyers: Persons whose profession is to give legal advice and assistance to clients and represent them in legal matters. (American Heritage Dictionary, 3d ed)Child Advocacy: Promotion and protection of the rights of children; frequently through a legal process.Questionnaires: Predetermined sets of questions used to collect data - clinical data, social status, occupational group, etc. The term is often applied to a self-completed survey instrument.Attitude of Health Personnel: Attitudes of personnel toward their patients, other professionals, toward the medical care system, etc.Bites, Human: Bites inflicted by humans.

Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism. (1/2)

Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using "crystal harvesting" and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 A, two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 A and 1.15 A, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 A resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct.  (+info)

Assessing the impact of denitrifier-produced nitric oxide on other bacteria. (2/2)

A series of experiments was undertaken to learn more about the impact on other bacteria of nitric oxide (NO) produced during denitrification. The denitrifier Rhodobacter sphaeroides 2.4.3 was chosen as a denitrifier for these experiments. To learn more about NO production by this bacterium, NO levels during denitrification were measured by using differential mass spectrometry. This revealed that NO levels produced during nitrate respiration by this bacterium were in the low muM range. This concentration of NO is higher than that previously measured in denitrifiers, including Achromobacter cycloclastes and Paracoccus denitrificans. Therefore, both 2.4.3 and A. cycloclastes were used in this work to compare the effects of various NO levels on nondenitrifying bacteria. By use of bacterial overlays, it was found that the NO generated by A. cycloclastes and 2.4.3 cells during denitrification inhibited the growth of both Bacillus subtilis and R. sphaeroides 2.4.1 but that R. sphaeroides 2.4.3 caused larger zones of inhibition in the overlays than A. cycloclastes. Both R. sphaeroides 2.4.3 and A. cycloclastes induced the expression of the NO stress response gene hmp in B. subtilis. Taken together, these results indicate that there is variability in the NO concentrations produced by denitrifiers, but, irrespective of the NO levels produced, microbes in the surrounding environment were responsive to the NO produced during denitrification.  (+info)

1NIC: The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted.
1NIE: The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted.
McMahons biggest defense for extinction of all carnivores is that it would be good to prevent the vast suffering and countless violent deaths caused by predation. His assumption that the end of all suffering deaths caused by predation is a good thing fails on two accounts. First, he fails to take into account "predation" in the microbial level. Numerous bacteria on Earth that kill other bacteria are vital to all living organisms. Virtually all, living organisms house predatory bacteria that feed on other bacteria in order to multiply. However, these bacteria also decompose harmful pathogens and aid in absorbing nutrients for survival. For example, in Humans, lactic acid bacteria kill pathogens in the stomach that cause diarrhea. In fact, the elimination of all predating microbes would wipe out all living creatures on earth due to diseases. Although according to McMahon, these causes "animal suffering", most people would not desire the elimination of all predating bacteria. Suppose McMahon ...
2. Proteomics analysis has been initiated (Clare Rutherford Honours student) for analysis of response of Psychroflexus torquis to light and dark conditions grown at 2 C (grown in a modified marine medium). The proteomics involves shotgun analysis using a 2-dimensional HPLC separation of trypsinised protein extracts (recovered using the QProteome proteoin extraction kit and extraction with membrane protein surfactant C7BzO, Sigma-Aldrich) coupled to nano-flow LTQ-Orbitrap mass spectrometry. This work is done in collaboration with Dr Edwin Lowe, Central Sciences Laboratory. The goal of this experiment is to determine whether the presence of light induces PR translation (abundance) and it cognate carotenoid hydroxylase as well as other changes to the proteome. Based on recent experiments on other bacteria (E. coli and L. monocytogenes) as much as 50% of the proteome can be recovered using this approach (termed "MudPit" - multidimensional protein information technology). This will be first time such ...
Author: Taschner, Michael et al.; Genre: Journal Article; Published in Print: 2012-11-27; Keywords: HISTONE DEACETYLASE INHIBITORS; MICROTUBULES; SUPERFAMILY; MECHANISMS;|br/| P300/CBP; DOMAIN; SITEcilium; crystal structure; post-translational modification; ; Title: Atomic resolution structure of human alpha-tubulin acetyltransferase|br/| bound to acetyl-CoA
Human pheromones dont really have a strong scent. The myth that by applying deodorant, you are covering up your natural pheromones doesnt hold much water. Most people would definitely prefer the smell of deodorant over strong body odor. Technically, pheromones are odorless; they are more or less "detected" by an organ in your nose called the vomeronasal organ. This organ, though more developed in other mammals, sends signals to the brain when pheromones are detected that may say things like, "Whoa, healthy genes at 8 oclock, lets get his number." At least thats what buyers of these products hope ...
Predatory bacteria are ubiquitous in aquatic environments and may be important players in the ecology and biogeochemistry of microbial communities. Three novel strains belonging to two genera of marine flavobacteria, Olleya and Tenacibaculum, were cultured from coastal sediments and found to be predatory on other bacteria on surfaces. Two published species of the genus Tenacibaculum were also observed to grow by lysis of prey bacteria, raising the possibility that predation may be a widespread lifestyle amongst marine flavobacteria, which are diverse and abundant in a variety of marine environments. The marine flavobacterial clade is known to include species capable of photoheterotrophy, scavenging of polymeric organic substances, pathogenesis on animals, the degradation and lysis of phytoplankton blooms and, now, predation on bacterial communities. Strains from the two genera were found to exhibit divergent prey specificities and growth yields when growing predatorily. Olleya sp. predatory ...
Image shows swarm of M. xanthus bacteria (left) invading a colony of prey bacteria (right). The rippling pattern is the highly organized behavior of thousands of M. xanthus cells working in concert to digest the prey. Image courtesy of John Kirby, University of Iowa Carver College of Medicine Like something from a horror movie, the swarm of bacteria ripples purposefully toward their prey, devours it and moves on. Researchers at the University of Iowa are studying this behavior in Myxococcus xanthus (M. xanthus), a bacterium commonly found in soil, which preys on other bacteria.. Despite its deadly role in the bacterial world, M. xanthus is harmless to humans and might one day be used beneficially to destroy harmful bacteria on surfaces or in human infections, said John Kirby, PhD, associate professor of microbiology in the UI Roy J. and Lucille A. Carver College of Medicine. It may be that we can modify this predator-prey relationship or apply it to medically relevant situations, Kirby said. ...
Any commercially-produced bottle of wine will say Contains sulfites. Our wines are all low in sulfites, but what are sulfites, and how do they effect you?
This module explores advanced aspects of protein science - including protein structure and function, determination of structure and protein engineering. Our appreciation of almost all aspects of biochemistry and molecular biology has been enhanced by the elucidation of atomic resolution structures that reveal the underlying chemical mechanisms responsible for biological function. In addition, our ability to exploit this understanding through the use of genetic approaches to engineer proteins, is leading to the generation of improved proteins for therapeutic and biotechnology applications. Students studying this module will be equipped to go on to further studies in biochemistry/molecular biology related fields of study, as well as having valuable insight into the growing biotechnology sector of industry.. ...
ProCrystal covers are designed for high-throughput protein x-ray crystallography to generate atomic resolution structures of protein molecules. The seals sit directly over the microplate crystallization wells. The seals are validated to be incorruptible and materials will not ingress into samples. They are available
in either an individual well pre-cut format so that one can easily remove crystals using a forceps from individual wells without affecting neighboring wells or uncut format. They are exceptionally hydrophobic which maintains drop footprint and segregation even with the use of MPD, Glycerol, ordetergents.

  • Two formats: individually cut and removable reagent well seals or single sheet, uncut seals
  • UV compatible
  • No noticeable x-ray diffraction
  • Accommodates up to 3 protein drops per well
Cryo-electron microscopy is used to discover, or "resolve", protein structure. This procedure is a neat tool for imaging proteins that are reluctant to crystallize. It is done by freezing a batch of proteins in liquid ethane and then imaging the non-crystalline ice. Specifically, Walls collects about 1500 micrograph images of the frozen, tumbling proteins in 48 hours. Cryo-EM uniquely enables looking at biological macromolecules in a near-native state, since they are frozen in the shapes that they take on in everyday life. With these images in tow, Walls can then use highly parallelized algorithms to solve for the proteins atomic resolution structures - ultimately a list of amino acid coordinates in three dimensions. The algorithms align, unblur, and average the 2D images of the proteins, and the more images there are of proteins at slightly different tilts and conformations, the more precise the 2D class averages will show the various orientations. The more precise these 2D classes are, the ...
"The 2.3 angstrom X-ray structure of nitrite reductase from Achromobacter cycloclastes". Science. 253 (5018): 438-442. doi: ...
Achromobacter MeSH B03.660.075.027.030.100 --- Achromobacter cycloclastes MeSH B03.660.075.027.030.120 --- Achromobacter ... Achromobacter cycloclastes MeSH B03.440.400.425.117.024.120 --- Achromobacter denitrificans MeSH B03.440.400.425.117.050 --- ...
... is a Gram-negative, aerobic bacterium from the genus Achromobacter. The complete genome of A. ... cycloclastes has been sequenced. List of sequenced bacterial genomes Uniprot straininfo of Achromobacter cycloclastes NCBI ...
Achromobacter cycloclastes is a Gram-negative, aerobic bacterium from the genus Achromobacter. The complete genome of A. ... cycloclastes has been sequenced. List of sequenced bacterial genomes Uniprot straininfo of Achromobacter cycloclastes NCBI ...
The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II ... Achromobacter cycloclastes EC#: 1.7.2.1 IUBMB Details: PH 6.0 ("KP") Gene Name(s): nirK ... THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU ...
Achromobacter cycloclastes. Sarcina lutea. Kluyvera citrophila. Pseudomonas fluorescens. Micrococcus lysodeikticus.. The ...
Source organism: Achromobacter cycloclastes. Primary publication:. Atomic resolution structures of resting-state, substrate- ... Source organism: Achromobacter cycloclastes. UniProt: *Canonical: P25006 (Residues: 39-378; Coverage: 100%) ... Atomic Resolution Structure of Achromobacter cycloclastes Cu Nitrite Reductase with Endogenously bound Nitrite and NO. ...
Achromobacter cycloclastes copper dependent nitrite reductase (nir) gene,partial cds. ATCC 21921 ... Achromobacter cycloclastes regulatory protein NosR (nosR), nitrous oxidereductase precursor (nosZ), accessory protein NosD ...
PDB references: Achromobacter cycloclastes nitrite reductase, data set ds1240K, 5n8f; data set ds2240K, 5n8g; data set ds3240K ... Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase. ...
SEQ ID NO: 5. Amino acid sequence of pseudoazurin from Achromobacter cycloclastes. ... SEQ ID NO: 7. Amino acid sequence of azurin from Achromobacter xylosoxidans ssp. denitrificans I. ... In particularly specific embodiments, the azurin is derived from Pseudomonas aeruginosa, Alcaligenes faecalis, Achromobacter ... In particularly specific embodiments, the azurin is derived from Pseudomonas aeruginosa, Alcaligenes faecalis, Achromobacter ...
Achromobacter cycloclastes and Alcaligenes faecalis) NiRs which have been extensively studied and may indicate that these also ...
Crystallization and preliminary X-ray studies on pseudoazurin from Achromobacter cycloclastes IAM1013.. J. Biochem. 114 761-2 ... Crystal structure determinations of oxidized and reduced pseudoazurins from Achromobacter cycloclastes. Concerted movement of ...
The accession numbers of the nosZ genes are as follows: Achromobacter cycloclastes, AF047429 ; Bradyrhizobium japonicum, ... Achromobacter cycloclastes-Bradyrhizobium japonicum (199 bp), Paracoccus denitrificans (153 bp), and Rhodobacter sphaeroides ( ... Achromobacter group); however (as with the amoA genes), the nosZ sequences all cluster at the periphery of the various known ... Achromobacter sp., and Sinorhizobium sp.) and environmental nosZ sequences in the GenBank database. The similarities ranged ...
Species: Achromobacter cycloclastes [TaxId:223]. Gene: nirK. Database cross-references and differences (RAF-indexed): *Uniprot ...
"The 2.3 angstrom X-ray structure of nitrite reductase from Achromobacter cycloclastes". Science. 253 (5018): 438-442. doi: ...
Publications] T.Inoue: Crystallization and Preliminary X-ray Studies on Pseudoazurin from Achromobacter cycloclastes IAM 1013 ... Publications] T.Kohzuma: Direct Electrochemistry of Nitrite Reductase from Achromobacter cycloclastes IAM 1013. Bull.Chem.Soc ... Publications] T.Kohzuma: Direct Electrochemistry of Copper-Containing Nitrite Reductase from Achromobacter xylosoxidans NCIB ...
Induction of denitrifying enzymes in oxygen-limited Achromobacter cycloclastes continuous culture. FEMS Microbiol. Ecol. 73:263 ...
... the quaternary structure and enzyme activity of the nitric oxide forming nitrite reductase from Achromobacter cycloclastes. ...
... rebound mechanism for production of N2O from nitrite by the copper-containing nitrite reductase from Achromobacter-Cycloclastes ...
Achromobacter cycloclastes (Z48635), Pseudomonas aureofaciens(Z21945), Pseudomonas sp. strain G-179 (M97294),Rhodobacter ... of uncharacterized dNir type were screened with this combination and an antiserum against Cu dNir from Alcaligenes cycloclastes ...
Achromobacter cycloclastes 37538302, and Anaeromyxobacter dehalogenans 2CP-C 86158824) was built with HMMER 3.0 and used to ...
The 2.3 angstrom X-ray structure of nitrite reductase from Achromobacter cycloclastes. Science 253 (1991) 438-442. [PMID: ... 3. Prakash, O.M. and Sadana, J.C. Purification, characterization and properties of nitrite reductase of Achromobacter fischeri ...
Achromobacter cycloclastes. Pharmacological action. Unknown. General Function. Nitrite reductase (no-forming) activity. ...
Achromobacter cycloclastes molecule tags Oxidoreductase molecule keywords Copper-containing nitrite reductase total genus 91 ...
Achromobacter cycloclastes. 13.4. 260. Amycianin. Thiobacillus versutus. 13.8. 261. Azurin. Alcaligenes denitrificans. 14.0. ...
Achromobacter cycloclastes. Mutation(s): 0 Gene Names: nirK. EC: 1.7.2.1. Find proteins for P25006 (Achromobacter cycloclastes) ...
Achromobacter cycloclastes molecule tags Oxidoreductase molecule keywords Copper-containing nitrite reductase total genus 92 ...
  • 8. The pharmaceutical composition of claim 4 , wherein the cupredoxin peptide is from an organism selected from the group consisting of Pseudomonas aeruginosa, Alcaligenes faecalis, Achromobacter xylosoxidan, Bordetella bronchiseptica, Methylomonas sp. (google.com)
  • Crystal structure determinations of oxidized and reduced pseudoazurins from Achromobacter cycloclastes. (ebi.ac.uk)