bluuebunny/crossref_metadata_2025 huggingface dataset:
Inducible Nitric Oxide Synthase
Authors: Rosenfeld Robin J , Tainer John A , Getzoff Elizabeth D
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification, and Molecular Characterization

Activity Tests

Metal Content and Cofactors

Spectroscopy

X‐Ray Structures

Functional Aspects

Functional Derivatives

Intramolecular Electron Transfer and Catalytic Mechanism

Acknowledgements

Related Articles
Endothelial Nitric Oxide Synthase
Authors: Raman C S
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification and Molecular Characterization

Metal Content and Cofactors

Activity Test

Spectroscopy

X‐Ray Structure

Interdomain Electron‐Transfer and Catalysis

Related Articles
Heme Oxygenase
Authors: Schuller David J
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification and Molecular Characterization

Metal Content and Cofactors

Activity Test

Spectroscopy

X‐Ray Structures of MammalianHO‐1 with Heme

Functional Aspects

Catalytic Mechanism

Related Articles
Bacterial CytochromecOxidase
Authors: Kannt Aimo , Michel Hartmut
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production and Purification

Metal Content and Cofactors

Activity Test

Spectroscopy

X‐Ray Structure of Bacterial CytochromecOxidase

Crystallization

Overall Description of the Structure

Functional Aspects

Related Articles
Mitochondrial Cytochrome

c

Oxidase
Authors: Yoshikawa Shinya , Shinzawa‐Itoh Kyoko , Yamashita Eiki , Tsukihara Tomitake
Published: December 2011

Cytochrome
c
oxidase reduces molecular oxygen (O
2
) to water (coupled with proton pumping) at its O
2
reduction site composed of an iron ion (heme
a
3
) and a copper ion (Cu
B
) by electrons transferred from cytochrome
c
in the intermembrane space by Cu
A
and heme
a
in the enzyme protein and by protons from the matrix space. Mitochondrial cytochrome
c
oxidase, isolated from bovine heart muscle as early as in 1941, was crystallized to determine the X‐ray structure at 2.3/2.35 Å resolutions in the fully oxidized/reduced states in 1998, showing 13 different subunits and Cu
B
, liganded with three histidine imidazole groups in a trigonal‐planer coordination in the fully reduced state. A tyrosine phenol group is fixed close to the O
2
reduction site with a covalent link with one of the three imidazole groups. This O
2
reduction site structure suggests that Fe

a
3

O
2
and Fe

a
3

OOH are stable and unstable, respectively, to form FeO as the second intermediate in the O
2
reduction process, consistent with the resonance Raman results for the process. A fairly big redox‐coupled X‐ray structural change in an aspartate (Asp51) located near the intermembrane surface of the enzyme molecule suggesting a large redox‐coupled pKa change in Asp51 and a hydrogen bond network connecting Asp51 with the matrix surface indicate that Asp51 is the site for proton pumping. A peptide bond in the hydrogen bond network facilitates the unidirectional proton transfer through the hydrogen bond network up to Asp51.
ba3‐CytochromecOxidase FromThermus Thermophilus
Authors: Than Manuel E , Soulimane Tewfik
Published: December 2011

ba3‐Cytochromecoxidase fromThermus thermophilusis a terminal enzyme of respiration that catalyzes the reduction of dioxygen to water. It is produced at low oxygen tension and is one of the most divergent members of the heme–copper oxidase superfamily.ba3‐Oxidase has been isolated fromT. thermophilusmembranes, purified and characterized using several biochemical and biophysical techniques. Its crystal structure has been solved at high resolution. The current review summarizes the results on structure and function relationship ofba3‐oxidase that have been elucidated during the last decade.
Cytochromebc1Complex
Authors: Link Thomas A
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification and Molecular Characterization

Metal Content and Cofactors

Activity Test

Spectroscopy

X‐Ray Structure

Functional Aspects

Functional Derivatives

Catalytic Mechanism
Hydroxylamine Oxidoreductase
Authors: Igarashi Noriyuki , Tanaka Nobuo
Published: December 2011

Ammonium oxidizing bacteria acquire their growth energy by oxidizing ammonia to nitrate. Hydroxylamine oxidoreductase (HAO), a periplasmic multi‐heme enzyme, shoulders the central role of this respiratory system by catalyzing the four‐electron oxidation from hydroxylamine to nitrite. Spectroscopic, catalytic, and crystallographic studies on HAO have been performed in detail for many years. The crystal structure of HAO fromNitrosomonas europaeashowed that the molecule is a homotrimer containing a total of 24 hemes, which form a branched chain. The structure also revealed a unique catalytic center known as heme P460, and suggested the plausible sites of cytochrome binding on the molecular surface.
Sulfite Reductase Hemoprotein
Authors: Elizabeth Stroupe M , Getzoff Elizabeth D
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification, and Molecular Characterization

Metal Content and Cofactors

Activity Assay

Spectroscopy

Crystallography and Structure of NativeSiRHP

Functional Aspects

Relationship between Structure and Redox States: Implications for Catalysis

Conclusions

Note Added in Proof

Acknowledgments
FeSRieske Center
Authors: Link Thomas A
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Biosynthesis

Protein Production, Purification and Molecular Characterization

Metal Content and Cofactors

Activity Test

Spectroscopy

X‐Ray Structure

Functional Aspects

Functional Derivatives

Catalytic Mechanism

Related Articles
Ferredoxins Containing Two DifferentFe/SCenters of the Forms [4Fe–4S] and [3Fe–4S]
Authors: Stout Charles D
Published: December 2011

This article reviews 7Fe ferredoxins (Fds), [FeS] proteins that contain [3Fe–4S]+/0and [4Fe–4S]2+/+clusters. The 7Fe Fds from 19 prokaryotes are described in terms of biological function, and categorized with respect to cysteine ligand motifs, length of amino‐acid sequence, and metal ion content. Biochemical, mutagenesis, electrochemical, spectroscopic, and crystallographic data are summarized for well‐studied examples of distinct subclasses, including 7Fe Fds fromAzotobacter vinelandii,Desulfovibrio africanus,Bacillus schlegelii, andSulfolobus acidocaldarius. 7Fe Fds have been used to study cysteine ligand motifs, the interconversion of [3Fe–4S] and [4Fe–4S] clusters, proton transfer to [3Fe–4S]0clusters, and the protein control of [FeS] cluster reduction potential.
The 2[4Fe–4S] Ferredoxins
Authors: Sieker Larry C , Adman Elinor T
Published: December 2011

The 2[4Fe4S] ferredoxins, that are members of the ‘clostridial’ and ‘chromatium’ classes of bacterial ferredoxins, have two cuboidal 4Fe4S clusters each in which each iron is coordinated by three inorganic sulfurs and one cysteinyl sulfur. The protein chains (54–80 amino acids) have internal homology so that the environments of each cluster are similar, and the 12.5 Å center‐to‐center separation of the clusters permits electronic interaction. These proteins participate in electron transfer systems, and, characteristically, have very low redox potentials. NH‐S hydrogen bonds, peptide dipole orientations, and solvent accessibility are among factors that have an effect on the oxidation–reduction potential. In that regard, a ‘spine’ of water molecules seems to be a conserved structural component linking the β‐sheet in each half of the molecule for all the ferredoxins in this class. Site‐directed mutagenesis studies have been carried out to analyze redox potentials, stability, intermolecular interactions, and intramolecular electron transfer.
Hybrid Cluster Protein
Authors: Bailey Susan , Cooper Serena J , Hagen WF , Arendsen AF , Lindley Peter F
Published: December 2011

Genes encoding hybrid cluster proteins (HCPs) are widespread among bacterial and archaeal species and are found within the nitrate assimilation gene region. The crystal structure of HCP from

Desulfovibrio vulgaris

(Hildenborough) reveals two 4Fe clusters with an edge‐to‐edge distance of 10.9 Å. The first cluster is a conventional [4Fe4S] cubane cluster. The second cluster has an unusual asymmetric structure and has been named the hybrid cluster to reflect the variety of protein ligands. Both the hybrid cluster and the cubane cluster give rise to unusual EPR signals and the hybrid cluster has four stable oxidation states. The physiological role of HCP is currently uncertain, although HCP from

Rhodobacter capsulatus

catalyzes hydroxylamine reduction, suggesting a role in the assimilation of hydroxylamine.
Protocatechuate 3,4‐Dioxygenase
Authors: Ohlendorf Douglas H , Vetting Matthew W
Published: December 2011

A key step in the degradation of aromatic compounds in the biosphere is the ring‐opening step. Intradiol dioxygenases typically use a nonheme ferric iron to activate the substrate for an electrophilic attack by molecular oxygen to cleave catechol derivatives between the vicinal hydroxyls. Protocatechuate 3,4‐dioxygenase (PCD) has been the most thoroughly studied of the intradiol dioxygenases because of the presence of optical and electron paramagnetic resonance (EPR) spectroscopic signals. The structures of PCD fromPseudomonas putidaandAcinetobacter calcoaceticusalone and in complexes with more than a dozen substrates and inhibitors have been used to visualize steps in substrate binding and ligand dissociation.
FeSuperoxide Dismutase
Authors: Miller Anne‐Frances
Published: December 2011

Iron‐containing superoxide dismutases (FeSOD) are generally dimers of identical 21‐kDa monomers, each of which contains a single active site. Each active site binds one Fe ion with roughly trigonal bipyramidal geometry, employing two His and an Asp−residue as equatorial ligands, and one more His and a coordinated solvent as axial ligands. In the course of the catalytic cycle, the Fe alternates between the +3 and +2 states, and the coordinated solvent is believed to alternate between OH−and H2O, in concert. Activity is inhibited by coordination of F−, N3−, or OH−to the oxidized state. Decreased activity at high pH reflects the latter in addition to ionization of the conserved Tyr34 in the reduced state of the enzyme at pH 8.5. Despite strong structural homologies with the manganese containing superoxide dismutases (MnSODs), many FeSODs are inactive when reconstituted with Mn, and in the case ofEscherichia coliSODs this appears to reflect, at least in part, very large differences in the reduction potentials produced by the two different SOD proteins, either Fe or Mn. Subtle changes in strengths of key active site H‐bonds could differently tune the pKs of the coordinated solvent molecule, whose participation in proton‐coupled electron transfer would in turn cause these differences to contribute to different reduction potentials, in the two proteins. Thus, SOD suggests that H‐bond mediated tuning of the protonation state and pKs of redox‐coupled coordinated solvents may serve as a means of tuning the Emin other cases as well.
Ribonucleotide Reductase
Authors: Eklund Hans
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid and Sequence Information

Protein Production, Purification and Molecular Characterization

Metal Content and Cofactors

Activity Test

Spectroscopy

X‐Ray Structure ofE. ColiR2

X‐Ray Structure ofE. ColiR1

Crystal Structure ofS. TyphimuriumR2

Crystal Structure of MouseR2

Functional Aspects

Functional Derivatives

Tyrosyl Radical Site

Oxidation of Tyrosine 122 to a Radical Species

Catalytic Mechanism

Related Articles
Δ9Stearoyl‐Acyl Carrier Protein Desaturase
Authors: Lindqvist Ylva
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification and Molecular Characterization

Metal Content and Cofactors

Activity Test

Spectroscopy

X‐Ray Structure of Δ9Stearoyl‐Acyl Carrier Protein Desaturase

Functional Aspects

The Catalytic Mechanism

Acknowledgements

Related Articles
Cytochromeb1– Bacterioferritin
Authors: Frolow Felix , Kalb(Gilboa) Aaron Joseph
Published: December 2011

Cytochrome b1, also known as bacterioferritin, has been isolated fromEscherichia coli, as well as many other bacteria. This large 400‐kD protein is composed of 24 identical subunits arranged in a shell of cubic (432) symmetry and contains at least three distinct forms of iron:

12 heme irons coordinated by pairs of methionine sulfurs from contiguous twofold symmetry related subunits

48 iron atoms, two in each subunit, occupying aquasi‐symmetric binuclear metal‐binding site

several thousand bulk iron atoms that may be deposited as a microcrystalline polymeric mineral in the hollow interior of the ferritin‐like protein shell.
Transferrins
Authors: Lindley Peter F
Published: December 2011

There 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

FhuA, 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

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification and Molecular Characterization

Metal Content and Cofactors

Activity Test

Three‐Dimensional Structures

Functional Aspects

Related Articles
Urease
Authors: Hausinger Robert P , Karplus P Andrew
Published: December 2011

Urease 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

Ni–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

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification, and Molecular Characterization

Metal Content and Specificity

Activity Test

Spectroscopy

Crystallography and Structure

Functional Aspects

Functional Derivatives

Conclusions

Related Articles
Arginase
Authors: Bewley Maria C , Flanagan John M
Published: December 2011

Arginase 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

The 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

Dimethylsulfoxide 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

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

Plastocyanin 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

An 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

Rusticyanin 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

The 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

The 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

(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

The 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

Octaheme 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

Cytosolic 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

Development 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

The 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

Carbon 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.
Fts
H
/
Hfl
B
Authors: Bieniossek Christoph , Baumann Ulrich
Published: December 2011

The ATP‐dependent, membrane‐standing metalloprotease FtsH/HflB (filamentation temperature‐sensitive locus H/high frequency of lysogenisation locus B) is universally conserved in eubacteria, chloroplasts, and mitochondria. Its substrates are integral membrane proteins, for example, it degrades the unassembled subunits such as SecY of the SecYEG translocon or the a‐subunit of F
o
ATPase, as well as some soluble proteins, most notably the heat shock factor σ
32
, the λ‐phage transcriptional activator λ‐CII and LpxC, a key enzyme in lipid A biosynthesis. FtsH is the only essential energy‐dependent protease in
Escherichia coli
and its knockout shows generally severe phenotypes, for example, malfunctioning of paraplegin, a close homolog in human mitochondria, results in one form of spastic paraplegia. The crystal structure of the cytosolic region reported here reveals a self‐compartmentalizing protease composed of two hexameric rings. The protease ring exhibits perfect sixfold symmetry with a novel, virtually all‐helical fold of the monomers. The active center is formed by the
427
HEAGH motif and the conserved Asp500 as third zing ligand. The AAA domains have ADP bound and are arranged in a hexameric ring with twofold symmetry only. Two of the essential pore residues Phe234, which are implied in substrate binding and translocation, are located toward the interior of the two rings. This suggests a mechanism of substrate recognition and unfolding.
Copper Transporters and Chaperones
Authors: Arnesano Fabio , Banci Lucia
Published: December 2011

Copper is an essential element for many cellular processes in all the kingdoms of life. Its presence in cells needs to be tightly controlled, as free copper ions can be toxic due to their redox chemistry, though they must be available to obtain the mature form of copper‐dependent proteins.

For this purpose, organisms have developed a machinery for proteins, which control copper uptake, transport, sequestration, and efflux. These proteins are engaged in complex, highly specific pathways, responsible for copper incorporation in target proteins, its transport within a compartment and/or through different cellular compartments and organelles, and its excretion. In the present chapter, we describe the structural and functional features of proteins involved in the three most characterized processes, that is, copper delivery to the trans‐Golgi network or transport across the plasma membrane, involving copper‐transporting adenosine triphosphatases, copper incorporation into the Cu,Zn superoxide dismutase, and into the two copper centers of cytochromecoxidase, located in two different enzyme subunits and involving three copper ions.

The structural properties of various functional states of these copper transport proteins, and the related mechanisms, are discussed with respect to their key role in cellular processes.
Pyruvate–Ferredoxin Oxidoreductase
Authors: Chabriere Eric , Cavazza Christine , Contreras‐Martel Carlos , Fontecilla‐Camps Juan C.
Published: December 2011

Pyruvate decarboxylation in many anaerobic organisms is catalyzed by the thiamine diphosphate (ThDP)‐dependent pyruvate–ferredoxin oxidoreductase. We have determined the native structure of this ancient enzyme, as well as of several reaction intermediates, by soaking crystals in a pyruvate‐containing solution. As the reaction progresses, ThDP approaches the substrate and cleaves a CC bond generating an acetyl‐ThDP radical intermediate and CO2. The comparison of this structure with a similar intermediate in transketolase (TK), another ThDP‐dependent enzyme, reveals significant differences in the cofactor conformation.
Indoleamine 2,3‐Dioxygenase and Tryptophan 2,3‐Dioxygenase
Authors: Thackray Sarah J , Bruckmann Chiara , Mowat Christopher G , Forouhar Farhad , Chapman Stephen K , Tong Liang
Published: December 2011

Indoleamine 2,3‐dioxygenase (IDO) and tryptophan 2,3‐dioxygenase (TDO) are heme‐containing enzymes from a small family of homologous enzymes. Despite both catalyzing the dioxygenation ofL‐tryptophan, the first step in the kynurenine pathway, the sequence similarity between TDO and IDO is low. Alignment of sequences across this family of enzymes is only possible on the basis of their structures. Human IDO shows activity toward a wider range of substrates than TDO, and is found throughout the body, while TDO is limited to the liver and epidermis in mammals. To date, no functional prokaryotic IDO has been identified, while TDO is found in many bacteria. TDO and IDO have been implicated in a number of human physiological conditions, including suppression of T‐cell proliferation and the immune escape of cancers, making them attractive targets for drug discovery.
Thioredoxin‐Like [2Fe–2S] Ferredoxin
Authors: Meyer Jacques , Andrade Susana LA , Einsle Oliver
Published: December 2011

Thioredoxin‐like [2Fe–2S] ferredoxin (Trx‐like‐Fd) is a soluble homodimer of ca. 100‐residue subunits, each containing a [2Fe–2S] cluster. This cluster is redox active and shuttles between the diferric [2Fe–2S]2+and the ferric–ferrous mixed‐valence [2Fe–2S]+state. The four cysteine ligands of the cluster occur in an idiosyncratic Cys‐X10, 12‐Cys‐X29, 34‐Cys‐X3‐Cys pattern. The small size of this protein and the tight insertion of the Fe–S cluster within the protein framework suggest an electron transfer function. However, the dimeric structure and the presence of a protruding loop in the vicinity of the Fe–S cluster may be indicative of a regulatory function. Protein folds similar to the Trx‐like‐Fd monomer occur as domains or subunits in many redox enzymes. In these cases, a single copy of the polypeptide chain is present with anN‐terminal extension of ca. 100 residues, and the protruding loop is shorter or absent altogether. Trx‐like‐Fd has been studied in considerable detail by high‐resolution X‐ray crystallography, spectroscopy, and site‐directed mutagenesis. Its function, however, has so far remained unknown.
Calx‐β Domains
Authors: Hilge Mark
Published: December 2011

Calx‐β domains that display the architecture of a seven‐stranded β‐sandwich form a relatively new class of Ca2+binding domains and are most closely related to C2 domains. Depending on the presence of a few acidic key residues in their Ca2+binding sites, Calx‐β domains can bind up to four Ca2+ions with affinities ranging from 10−7to 10−4 M. Functionally, the two copies of Calx‐β domains present in the cytosolic loop of the Na+/Ca2+exchanger are most extensively investigated and act as sensors for intracellular Ca2+. However, the physiological role of the vast majority of Calx‐β domains, located in the extracellular matrix, is intriguing since Ca2+concentrations in this environment are generally high.
Nickel Regulatory Transcription Factor,NikR
Authors: Phillips Christine M , Drennan Catherine L
Published: December 2011

The variety of roles that transition metals fulfill within the cell is staggering, but the concentrations of these metals must be tightly regulated to maintain minimal requisite levels and simultaneously prevent metal‐induced oxidative stress or inappropriate metal‐binding events. A variety of bacteria control the concentration of the transition metal nickel using the transcriptional repressor NikR. To suppress the import of nickel, the NikR protein binds nickel ions, inducing NikR's affinity for a promoter region upstream of a gene encoding a nickel‐specific importer. This binding event blocks RNA polymerase from attaching to the DNA, preventing the expression of further nickel‐specific importers. A variety of biochemical, structural, and spectroscopic studies on NikR have provided interesting insight into the overall function and structure of this regulatory protein.
Nonheme Iron Halogenases
Authors: Blasiak Leah C , Drennan Catherine L
Published: December 2011

Nonheme iron halogenases require Fe(II), O
2
, α‐ketoglutarate (αKG), and a halide ion and catalyze halogenation at unactivated, aliphatic carbons on their substrates. The nonheme iron halogenase SyrB2, from

Pseudomonas syringae

, catalyzes chlorination of threonine during biosynthesis of the plant toxin syringomycin. The X‐ray crystal structure of SyrB2 revealed a mononuclear iron center coordinated by two histidine residues, bidentate αKG, and a chloride ion. Spectroscopic studies on the nonheme iron halogenase CytC3 from
Streptomyces
sp. RK95‐74 have implicated an iron(IV)‐oxo as a hydrogen atom abstracting species in a mechanism similar to the related nonheme iron dioxygenases.
Particulate Methane Monooxygenase
Authors: Rosenzweig Amy C
Published: December 2011

Particulate methane monooxygenase (pMMO) catalyzes the oxidation of methane to methanol in methanotrophic bacteria. The 300‐kDa pMMO enzyme is a trimeric integral membrane protein, comprising three copies each of three subunits: pmoB, pmoA, and pmoC. Purified pMMO contains both copper and iron, although some of the iron may be due to heme contamination. The copper stoichiometry ranges from 2 to 15 copper ions per 100‐kDa pMMO protomer, depending on the enzyme source. EPR spectra of whole cells, membrane‐bound, and purified pMMO consistently indicate the presence of type 2 Cu(II). According to XAS data, both Cu(I) and Cu(II) are present. EXAFS data reveal the presence of oxygen/nitrogen ligands and a short CuCu interaction at 2.5 Å that increases to 2.6 Å upon chemical reduction. Crystal structures of pMMO from two organisms have been reported. A soluble region consisting of six cupredoxin‐like β‐barrel structures is supported by 15 transmembrane helices. Three different metal centers have been detected crystallographically: a highly conserved dinuclear copper center, a nonconserved mononuclear copper center, and a site that can be occupied by zinc or copper. Although the identity of the pMMO active site remains unknown, some information regarding the mechanism has been obtained from substrate studies and computational work.
The Membrane‐Bound Nitrate Reductase
A
from Escherichia Coli:
Nar
GHI
Authors: Bertero Michela
Published: December 2011

The bacterium

Escherichia coli

is able to survive in a wide range of adverse environmental conditions. When oxygen is limited and nitrate is present,

E. coli

synthesizes a specific electron transfer chain to produce energy for its own survival. The chain is constituted by two membrane‐bound enzymes: the initial formate dehydrogenase FdnGHI and the terminal nitrate reductase NarGHI. Electrons are transferred from the formate oxidation site to the nitrate reduction site with a net translocation of protons across the cytoplasmic membrane. In the recent years, crystallographic studies have shed light on the structure and function of the two enzymes revealing a clear picture of the nitrate electron transfer chain at the atomic level. The present article focuses on the advances obtained on NarGHI, its function and architecture, and the eight redox cofactors that form like an electrical wire through all the enzymes, starting from the electron acceptor site to the catalytic center.