bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transferrins
Authors: Lindley Peter F 
Published: December 2011

AbstractThere are three major classes of transferrins; serum transferrins, ovotransferrins, and lactoferrins. The serum transferrins are responsible for the transportation of iron in serum and its delivery to cells by receptor‐mediated endocytosis. Ovotransferrins are found in the avian egg whites and are identical to their serum counterpart except for the attached carbohydrates, but cannot normally bind to mammalian receptors. Lactoferrins are found in numerous extracellular fluids and in the specific granules of polymorphonuclear lymphocytes and are known to be multifunctional. The transferrins are monomeric glycoproteins with an approximate molecular mass of 80 kDa, which adopt a bilobal structure. Each of the structurally homologous lobes contains two dissimilar domains with a single ferric iron‐binding site buried within the inter‐domain cleft. The uptake of iron is preceded by the uptake of the synergistic (bi‐)carbonate anion.
The Ferric Hydroxamate Uptake ReceptorFhuAand RelatedTonB‐Dependent Transporters in the Outer Membrane of Gram‐Negative Bacteria
Authors: Ferguson Andrew D , Coulton James W , Diederichs Kay , Welte Wolfram 
Published: December 2011

AbstractFhuA, receptor for ferrichrome‐iron inEscherichia coli, is a member of a family of integral outer membrane proteins, which together with the energy transducing TonB–ExbB–ExbD complex of the cytoplasmic membrane, mediate active transport of siderophores, Vitamin B12, and heme across the outer membrane of gram‐negative bacteria.In addition to transporting ferrichrome, FhuA acts as the primary receptor for several bacteriophages, the antibiotics albomycin and rifamycin CGP 4832, the cyclic peptide antibiotic microcin J25, and the bacterial toxin, colicin M.FhuA is a β‐barrel composed of 22 antiparallel β‐strands. Located within the β‐barrel is a structurally distinct domain, the ’cork’, consisting mainly of a four‐stranded β‐sheet and four short α‐helices. The focus of this review is an analysis of the relationship between the three‐dimensional structure of FhuA and its biological function as an energy‐dependent outer membrane transporter.
Iron‐Dependent Regulators
Authors: Feese Michael D , Pohl Ehmke , Holmes Randall K , Hol Wim GJ 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestThree‐Dimensional StructuresFunctional AspectsRelated Articles
Urease
Authors: Hausinger Robert P , Karplus P Andrew 
Published: December 2011

AbstractUrease catalyzes the hydrolysis of urea by all plants and many algae, fungi, and bacteria. The homohexameric enzyme from jack bean was crystallized in 1926 and shown to contain nickel in 1975, but the structure of the dinuclear metal site was first revealed in 1995 by using the heterotrimeric [(UreABC)3] bacterial enzyme fromKlebsiella aerogenes. A carbamylated lysine side chain and a water molecule bridge the nickel ions at each active site, with Ni‐1 also coordinated to two histidine side chains plus a terminal water and Ni‐2 bound to two histidines, one aspartate, and a terminal water. The kinetic properties and structures of various inhibited or mutant forms of the protein provide insights into the mechanism of urease catalysis.
Nickel–Iron Hydrogenases
Authors: Frey Michel , Fontecilla‐Camps Juan C , Volbeda Anne 
Published: December 2011

AbstractNi–Fe hydrogenases catalyze the cleavage or the production of the most simple of chemical compounds, molecular hydrogen. This review provides an overview of the literature on these enzymes that has been published before the year 2000. On the basis of atomic models plausible pathways of substrates and products are described, including a hydrophobic tunnel network for H2diffusion, a suitable arrangement of three iron–sulfur clusters for electron transfer, a network of buried water molecules, and a magnesium site that could be involved in proton transfer. A combination of protein crystallography, electron paramagnetic resonance, and Fourier transform infrared spectroscopic studies has allowed the elucidation of the unique architecture of the active site. This consists of a thiolate‐coordinated Ni–Fe unit involving one carbon monoxide and two cyanide ligands to the iron, leaving two metal coordination sites available for substrate binding. Understanding the catalytic mechanism of these fascinating enzymes might be helpful for the development of cheap catalysts for fuel cells working on H2or of cheaper production methods for this clean fuel.
Manganese Superoxide Dismutase
Authors: Stroupe M Elizabeth , DiDonato Michael , Tainer John A 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification, and Molecular CharacterizationMetal Content and SpecificityActivity TestSpectroscopyCrystallography and StructureFunctional AspectsFunctional DerivativesConclusionsRelated Articles
Arginase
Authors: Bewley Maria C , Flanagan John M 
Published: December 2011

AbstractArginase is a manganese hydrolase related to agmatinases, formiminoglutamases, and proclavaminate amidino hydrolase. It hydrolyzes L‐arginine to L‐ornithine and urea and occurs in bacteria, yeast, plants, invertebrates, and vertebrates. In mammalian species cytosolic type I and mitochondrial type II arginase are found. Type I arginases, located in the liver, catalyze the final step in the urea cycle. Type II arginases are extrahepatic and catalyze the same reaction as type I arginases, but due to their cellular location, give rise to different biological functions that center on regulating the levels of L‐arginine or L‐ornithine. For example, they are thought to regulate the concentrations of L‐arginine, a biosynthetic precursor of nitric oxide (NO), and thus, participate in the NO signaling pathway. By controlling the concentration of L‐ornithine, they affect the biosynthesis pathway of glutamate, proline, and polyamines. Arginase monomers have molecular weights of about 30 to 40 kDa and generally function as homo‐oligomers. All spectroscopic measurements have been made using the rat liver arginase and the Mn(II) EPR spectra are typical of μ‐ligand bridge spin‐coupled Mn2(II,II) centers.Crystal structures of rat andBacillus caldoveloxarginases have been determined. Rat liver arginase is a homotrimer. Each monomer of 323 amino acids has a globular shape and comprises an eight‐stranded parallel ß‐sheet packed on either side by helices to form a single α/ß domain. Each monomer contains its own active site. Two catalytic manganese ions, MnAand MnBare located at the bottom of the active site. MnAis coordinated by a histidine, three aspartates, and two water molecules. MnBis also coordinated by a histidine and three aspartates but by one water molecule only. One of the aspartates is bidentately coordinated (MnB), two others bridge both Mn ions, one with one side chain oxygen to both Mn ions, the other one with each side chain oxygen individually to each Mn ion. Both Mn ions display an octahedral coordination. TheB. caldoveloxarginase is a homohexamer with 32 point group symmetry. Each monomer contains 299 amino acid residues. Overall fold and active site geometry is very similar to that of the rat enzyme. Crystal structures of arginases in complex with L‐arginine, L‐lysine, L‐ornithine, and 2(S)‐amino‐6‐borohexanoic acid (ABH) have been determined and have helped, together with kinetic studies, to formulate a structure‐based catalytic mechanism for arginase in parallel to an EPR‐based mechanism.
Aldehyde Oxidoreductase (MOP)
Authors: João Romão Maria , Moura José JG 
Published: December 2011

AbstractThe aldehyde oxido‐reductase fromDesulfovibrio gigas(MOP) is a member of the xanthine oxidase family but simpler since it lacks the flavin–adenine dinucleotide (FAD) domain. It is composed of a single polypeptide chain of 907 amino acids and contains one molybdenum atom bound to a molybdopterin cytosine dinucleotide (MCD) cofactor, as well as two spectroscopically distinguishable [2Fe2S] clusters involved in electron transfer. The Mo atom is pentacoordinated by the two sulfurs of thecis‐dithiolene group of the molybdopterin, plus two oxo and one hydroxyl/water ligand. It hydroxylates a wide range of aldehydes with little specificity but its physiological role is not totally clear.
Dimethylsulfoxide Reductase
Authors: Li Hung‐Kei , Schindelin Hermann 
Published: December 2011

AbstractDimethylsulfoxide reductase is a molybdenum cofactor‐containing enzyme, which catalyzes the two‐electron reduction of dimethylsulfoxide to dimethylsulfide. The enzyme consists of a single polypeptide chain of 780 amino acids and contains no other cofactor besides the molybdenum cofactor. The overall fold of the enzyme is structurally organized into four domains, which are grouped around the cofactor. The molybdenum cofactor consists of two molybdopterin guanine dinucleotides, which are symmetrically ligating the molybdenum with their dithiolene groups. In the oxidized Mo(VI) form of the enzyme, an oxo group and a serine side chain complete the coordination sphere. The oxo group is the catalytically labile oxygen, which is replaced by an aquo or, possibly, a hydroxo ligand in the reduced Mo(IV) state.
Trimethylamine

N

‐Oxide Reductase
Authors: Iobbi‐Nivol Chantal , Haser Richard , Méjean Vincent , Czjzek Mirjam 
Published: December 2011

Abstract

Trimethylamine
N
‐oxide (TMAO) is a compound widely distributed in marine fish and invertebrates; and TMAO reducing enzymes are found not only in marine bacteria and photosynthetic bacteria living in ponds but also in enterobacteria. The various respiratory systems reducing TMAO, described so far, share a high level of homology either in their general structure, or in the regulation or mechanism of electron transfer. According to their content of molybdenum cofactor, the enzymes in charge of TMAO reduction are classified in the structural dimethylsulfoxide (DMSO) reductase family. TMAO reductases, however, in contrast to DMSO reductases are highly specific enzymes and reduce only their physiological substrate. The crystal structure was determined for the TMAO reductase from
Shewanella massilia
, and its structural differences with DMSO reductases in the environment of the active site. A tyrosine residue in the proximity of the molybdenum ion in DMSO reductases is absent in TMAO reductases and could be related to the differences in substrate specificities.
Plastocyanin
Authors: Freeman Hans C , Guss J Mitchell 
Published: December 2011

AbstractPlastocyanin was the first ‘blue’ or ‘type 1’ copper protein to be structurally characterized. Its biological role is to transfer electrons between photosystems II and I in oxygenic photosynthesis. Structures of plastocyanin from several plants, green algae, and cyanobacteria have been solved either by X‐ray diffraction or nuclear magnetic resonance (NMR) spectroscopy. Several of the structures have been determined with the copper atom in both the +1 and +2 oxidation states, and at several pH values. The polypeptide has a highly conserved β‐sandwich fold with a Greek‐key topology. The copper atom is coordinated by the side chains of two histidines, a cysteine, and a methionine.
Azurin and Azurin Mutants
Authors: Kolczak U. , Dennison C. , Messerschmidt A. , Canters G.W. 
Published: December 2011

AbstractAn overview is presented of the structural, spectroscopic, and mechanistic properties of the azurins, a sub‐class of the small blue copper proteins. Sequence information, methods to produce and purify the proteins, and structures as determined by X‐ray diffraction and nuclear magnetic resonance (NMR) are reviewed. The NMR and electron paramagnetic resonance (EPR) properties of the paramagnetic native and metal‐substituted azurins are discussed for wild type and variant (as obtained by site‐directed mutagenesis) forms. Electron transfer properties are discussed in the light of recent electron transfer theories.
Rusticyanin
Authors: Shoham Menachem 
Published: December 2011

AbstractRusticyanin is a type 1 blue copper protein that functions as the major electron carrier in the iron respiratory electron transport chain ofThiobacillus ferrooxidans. This bacterium is the main cause of acid mine drainage. Rusticyanin is an extremophilic protein with redox activity as low as pH 0.5 and a redox potential of 680 mV, which is at least twice as high as for any other member of the family of cupredoxins. The ligands to the single copper ion are His85, Cys138, His143, and Met148. The three‐dimensional structure consists of a β‐sandwich of two mixed β‐sheets, one of six and one of seven strands, as well as a single amphipathic helix near the N‐terminus.
Binuclear CopperA
Authors: Kroneck Peter MH 
Published: December 2011

AbstractThe purple CuA is a Cys‐bridged, mixed‐valence electron transfer center [Cu(1.5+)…Cu(1.5+)], found in cytochromecoxidase and in nitrous oxide reductase. More recently, the NO reductase fromBacillus azotoformanswas identified as the third CuA‐containing enzyme. There also exist engineered CuA sites which have been introduced by loop‐directed mutagenesis into blue type 1 copper proteins, such as azurin or amicyanin. Electron transfer mediated by CuA is very efficient. The reasons for utilizing a binuclear electron transfer center in cytochromecoxidase and nitrous oxide reductase, instead of mononuclear type 1 Cu, are suggested to be its unidirectional electron transfer through the site or the lower energy of reorganization. Interest in CuA is directly related to its unique spectroscopic properties. Studies by paramagnetic resonance, magnetic circular dichroism, resonance Raman, and X‐ray absorption spectroscopy have provided a clear picture of the electronic properties of the CuA site and the interaction of the metal atoms with the neighboring amino acids.
Yeast Copper Metallothionein
Authors: Peterson Cynthia W 
Published: December 2011

AbstractThe first structure of yeast copper metallothionein (1) was determined from solution NMR data using experimental NOEs and dihedral angle constraints along with specific metal to Cys connectivities derived for the isomorphic Ag(I) substituted Cu(I) yeast MT. In solution, both MTs bind seven moles of Cu(I) or Ag(I) ions, respectively, in a single cluster embedded in a cleft between two large parallel protein loops with only the metals on the open side of the cleft exposed to the solvent.It is reassuring to see the precision of the earlier solution structure compared to the recently published crystal structure (2) of a yeast copper thionein construct lacking the first 4 and last 13 residues of the intact protein. All of the crystal metal–Cys connectivities are identical to the previous solution structure, with the additional verification of the earlier postulated third Cys ligand to metal VI. The only difference is that the truncated, crystallized CuMT protein binds an eighth Cu(I) ion, labeled Cu39. (Note error in (2) where the “copper ion missing in solution structure” is misidentified as Cu44). Considering the fact that two of the three coordinating cysteines for Cu39 in (2) come from the N terminus, it is conceivable that cutting off four residues from this end enables an eighth metal to bind. Unfortunately, no solution study of the Cu(I) binding stoichiometry to this truncated form of the protein was reported. Naturally, the important structure is the structure of the native, full‐length yeast MT. We, therefore, recommend that caution be exercised before drawing any conclusions about the native protein structure on the basis of the crystal structure on the truncated yeast MT construct.
Nitrous Oxide Reductase
Authors: Eady Robert R , Antonyuk Svetlana V , Hasnain S Samar 
Published: December 2011

Abstract(N2O) is a major greenhouse gas and is thought to be some 300 times more potent than CO2in promoting global warming due to its inert chemical nature. The difficult chemistry of N2O reduction to gaseous nitrogen (N2) in biology is catalyzed by the novel µ4‐sulfide‐bridged tetranuclear Cuzcluster of the N2O reductases (N2ORs). These enzymes, in common with cytochrome c oxidase (CCO), also contain an electron‐donating CuAsite. During the past five years, several structures of this enzyme, from a number of species, have emerged, providing the details of structural elements responsible for this fascinating chemistry. These aspects are discussed in the light of extensive spectroscopic and functional data, providing an up‐to‐date review from these perspectives.
Amyloid Precursor Protein
Authors: Leong Su Ling , Barnham Kevin J. , Multhaup Gerd , Cappai Roberto 
Published: December 2011

AbstractThe amyloid‐precursor protein (APP) is a transmembrane glycoprotein implicated in the pathogenesis of Alzheimer's disease (AD). In mammals, there are two paralogues of APP termed amyloid precursor‐like protein 1 (APLP1) and amyloid precursor‐like protein 2 (APLP2). Orthologues of APP also exist, suggesting a conserved function vital throughout evolution. APP is a multidomain protein with metal‐binding sites critical to its function. There are two copper‐binding domains, one lies in the N‐terminus, adjacent to the zinc‐binding domain, and the other is in the amyloid‐beta (Aβ) domain. Aβ is derived via a series of protease cleavages of APP by the secretases, and is the main constituent of the amyloid plaques that are a key pathological hallmark of AD. The physiological role of APP is as yet unknown. It can reduce Cu2+to Cu+, and the physiological and three‐dimensional structure suggests a role as a copper chaperone. The binding of Cu to Aβ is toxic to neuronal cultures, and this may contribute to the oxidative stress that is commonly observed in AD.
Octaheme Tetrathionate Reductase
Authors: Mowat Christopher G. , Atkinson Sally J. , Reid Graeme A. 
Published: December 2011

AbstractOctaheme tetrathionate reductase (OTR) fromShewanella oneidensisis a soluble cytochrome with eight covalently attached heme groups. The gene encoding the protein has been cloned and overexpressed, and characterization of the protein is ongoing. From the crystal structure it can be seen that one of the hemes displays novel ligation of the iron atom by the ɛ‐amino group of a lysine residue. This occurs despite the heme attachment being via a typical CXXCH motif. It is believed that this heme represents the active site for tetrathionate reduction, a reaction which is catalyzed efficiently by the enzyme. Recent work has also suggested a multifunctional role for OTR, with the enzyme being demonstrated to catalyze the reduction of nitrite, hydroxylamine and nitric oxide.
Cytosolic Aconitase
Authors: Volbeda Anne , Moulis Jean‐Marc , Dupuy Jérôme , Walden William , Volz Karl , Fontecilla‐Camps Juan Carlos 
Published: December 2011

AbstractCytosolic aconitases (cAcns) have the remarkable property that they can function either as an enzyme or as a messenger (m) RNA‐binding protein. In the first case they contain a [4Fe–4S] cluster that is directly involved in the catalysis of the isomerization between citrate and isocitrate via acis‐aconitate intermediate. Upon loss of the cluster the enzymatic function is lost, the protein undergoes a substantial structural rearrangement and becomes capable of recognizing, with very high affinity, the so‐called iron‐responsive elements (IREs) in mRNAs. The latter code for proteins that are either dependent on Fe or are involved in the regulation of iron levels in the cell. The nonenzymatic form of cAcn is known as iron‐regulatory protein 1 or IRP1. Here we review the most recent structural data on the two forms, cAcn and IRP1, and correlate these with their respective functional properties. In addition, a comparison is made with closely related proteins like IRP2 and mitochondrial and bacterial aconitases.
Metal Ions in Cyanobacterial Photosystem II
Authors: Loll Bernhard , Biesiadka Jacek , Saenger Wolfram 
Published: December 2011

AbstractDevelopment of oxygenic photosynthesis provided the primeval reducing atmosphere with oxygen that is essential for all presently existing higher forms of heterotrophic life including human beings. Oxygenic photosynthesis is initiated at photosystem II (PSII), a multi‐subunit protein complex that is decorated with various cofactors and located in the thylakoid membrane of cyanobacteria, algae and higher plants. PSII captures sunlight with its antenna proteins and converts it to chemical energy by catalyzing water oxidation to atmospheric oxygen, protons and electrons. The reducing electrons are exploited in subsequent steps in the formation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) used to reduce CO2to carbohydrates.We discuss here the presently most complete structure of cyanobacterial PSII that includes 35 chlorophylla, 11 carotenoids, 2 pheophytinsa, 2 plastoquinones, 2 hemes, bicarbonate, 14 lipids, 3 detergent molecules (n‐dodecyl‐β‐D‐maltoside), 4 Mn‐atoms, 2 Ca2+, and Fe2+that are embedded within 19 protein subunits per monomer. Water oxidation takes place at a redox‐active metal cluster that is composed of 4 Mn‐cations and 1 Ca2+cation. The arrangement, geometry and coordination of the metal ions in the Mn4Ca‐cluster provide information essential for understanding mechanistic aspects of water oxidation.
CODehydrogenase/Acetyl‐CoASynthase
Authors: Fontecilla‐Camps Juan C , Volbeda Anne 
Published: December 2011

AbstractThe bifunctional tetrameric (α2β2) enzyme carbon monoxide dehydrogenase (CODH)/acetyl‐CoA synthase (ACS) is a central component of the Wood‐Ljungdahl pathway of acetogenic bacteria. In this pathway, two CO2molecules are reduced to a methyl group by folate‐containing enzymes and to CO by CODH, respectively. These two substrates are subsequently combined in ACS to form an Ni‐bound acetyl group that is reductively eliminated as acetyl‐CoA. The CODH and ACS active sites are about 70 Å apart and are connected by a network of hydrophobic tunnels. Thus, CO produced at the former enzyme migrates inside the bifunctional protein to the ACS site. Site‐directed mutagenesis has confirmed the functional role of the tunnels. The ACS subunit undergoes a conformational change that blocks the tunnel near the active site, preventing the escape of the toxic CO from within the enzyme upon methyl binding to nickel.
Ni,Fe‐Containing Carbon Monoxide Dehydrogenases
Authors: Jeoung Jae‐Hun , Dobbek Holger 
Published: December 2011

AbstractCarbon monoxide can be used by various aerobic bacteria, anaerobic bacteria, and archaea as their sole source of carbon and energy. Carbon monoxide dehydrogenases (CODHases) are the central enzymes in the use of carbon monoxide by microorganisms and they catalyze the reversible oxidation of carbon monoxide with water to carbon dioxide, two protons and two electrons. Two principal types of CODHases can be distinguished by their metal cofactors, sequences, specific activity, and stability in the presence of dioxygen. Whereas CODHases containing molybdenum, copper, iron, and flavin are found in aerobic bacteria, anaerobic microorganisms utilize oxygen‐sensitive CODHases containing nickel and iron. The active site of Ni,Fe‐containing CODHases harbors an asymmetric [NiFe4S4/5] cluster in which an Ni2+ion coordinated by three to four sulfur ligands is an integral constituent. A bimetallic site consisting of the Ni2+ion and a histidine and cysteine coordinated Fe2+ion (ferrous component II), located on one side of the cluster, is responsible for the binding and activation of carbon monoxide and water. In addition to the active site cluster, three [4Fe–S] clusters are found in the homodimer, of which one [4Fe–4S] cluster covalently links the two monomers.