bluuebunny/crossref_metadata_2025 huggingface dataset:
Metal‐Dependent TypeIIRestriction Endonucleases
Authors: Vanamee Éva Scheuring , Aggarwal Aneel K
Published: April 2006

Type II restriction endonucleases are phosphodiesterases that bind double‐stranded DNA with high specificity and cleave both strands of the DNA to yield 5′‐phosphate and 3′‐hydroxyl groups as products utilizing Mg2+as a cofactor. Owing to their high specificity and extraordinary number (>3500 discovered), type II restriction enzymes have become indispensable tools in molecular biology and have been widely exploited for studying site‐specific protein–DNA interactions. Surprisingly, they share little or no sequence homology among them, though the three‐dimensional structures of the 14 restriction enzymes determined to date reveal a common‐core motif with a central β‐sheet that is flanked by α‐helices on both sides. The active sites occur at one end of the central β‐sheet and contain at least three superimposable residues that are critical for catalysis. The cleavage reaction occurs through an SN2 mechanism with an in‐line displacement of the 3′‐hydroxyl group and an inversion of configuration of the 5′‐phosphate group. However, there is uncertainty about the precise mechanism of cleavage, especially regarding the number of metals involved in catalysis.
Cytochromec2
Authors: Miki Kunio , Sogabe Satoshi
Published: April 2006

Cytochromec2participates in biological processes, such as respiration and photosynthesis in bacteria, and reacts with a variety of proteins by transferring electrons in the manner of both oxidants and reductants, as in the reaction with ubiquinol‐cytochrome c oxidoreductase (cytochrome bc1complex) and the photosynthetic reaction center. Cytochromec2is found in the periplasmic space of the membrane, both in non‐sulfur purple photosynthetic bacteria and in non‐photosynthetic bacteria and serves as the bacterial counterpart of mitochondrial cytochromec. The molecule of cytochromec2exhibits a roughly globular shape with axial dimensions of 25 × 25 × 35 Å. The polypeptide folding is mostly composed of five α‐helical elements and fairly extended loops connecting helices. The protein fold envelops the heme prosthetic group within a hydrophobic pocket.
Cytochrome

c

6
Authors: Reuter Wolfgang , Wiegand Georg
Published: April 2006

Cytochrome
c
6
, or its functional analog copper protein plastocyanin, mediates the intrathylakoidal photosynthetic electron transfer from the always dimeric cytochrome
b
6
f
complex to the monomeric and/or trimeric Photosystem I (PS I) complex. The high‐potential monoheme protein belongs to the omnipresent cytochrome
c
family and is mainly characterized by its highly conserved N‐terminal heme coordinating sequence C–X–X–C–H and a low spin heme‐iron with methionine and histidine as axial ligands. Despite the excellent knowledge about synthesis, structures, and physical properties of cytochrome
c
6
from various organisms, the real molecular events that occur during its reduction by cytochrome
b
6
f
and its oxidation by the reaction center of PS I are presently uncertain. In addition, the specific role of cytochrome
c
6
within the hydrogen metabolism in an anaerobic environment is in the focus of interest. However, the presentation of established information about cytochrome
c
6
is accompanied by a brief discussion on the biochemical and physiological aspects concerning function, association, and changes of the molecule.
Cytochrome

c

4
Authors: Andersen Niels H , Christensen Hans EM , Iversen Gitte , Nørgaard Allan , Scharnagl Christina , Thuesen Marianne H , Ulstrup Jens
Published: April 2006

The di‐heme
c
‐type cytochrome
c
4
has been identified in the membrane space of a number of bacterial species, and the isolation and sequencing have been reported. The biological role is believed to be part of a respiratory chain. Recombinant cyt
c
4
from
Pseudomonas stutzeri
(190 residues) has become available since the publication of the chapter.

The 2.2 Å crystal structure has disclosed two almost equally sized globular domains, each with a His/Met axially coordinated heme group. Variable degrees of two‐fold structural symmetry can be distinguished. The relative heme group orientation is tilted with a short (2.6 Å) hydrogen bond between the propionate in each heme. The protein is strongly dipolar, with excess negative and positive charges of the N‐ and C‐terminal domains, respectively. UV/vis, nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), and resonance Raman spectral data point to distinct electronic features of the heme groups. The oxidized N‐terminal heme is in a mixed high‐spin/low‐spin state, while the reduced N‐terminal heme and both oxidized and reduced C‐terminal heme are in a pure low‐spin state. Chemically induced sequential unfolding of the domains also reflects selective domain properties.

As a two‐centre redox metalloprotein, cyt
c
4
offers a prototype case for mechanistic mapping of a multi‐centre redox protein. Electron transfer between cyt
c
4
and small reaction partners is multi‐phasic but the role of intramolecular electron transfer is inconclusive. Electrochemical electron transfer at low ionic strength, however, seems to involve unidirectional oxidation or reduction of the heme groups via intramolecular electron transfer. This may carry over to
in vivo
cyt
c
4
function in membrane environments.
Cytochromef
Authors: Soriano Glenda M , Smith Janet L , Cramer William A
Published: April 2006

Cytochromef(f, folium, leaf), ac‐type cytochrome with a characteristic CysXXCysHis amino acid sequence for heme ligation, is the largest of the four major protein subunits of the membrane‐embedded cytochromeb6fcomplex of oxygenic photosynthesis. It contains 285–86 amino acids, consisting of a soluble 250‐residue domain on the p‐side (positive‐side) or lumen‐side of the membrane, a single trans‐membrane 20‐residue α‐helix, and an n‐ or stromal‐side segment consisting of 15 residues. These domains contain, respectively, the heme prosthetic group and intraprotein electron transfer pathway, the membrane anchor and a short segment that is important in the assembly of theb6fcomplex.

The function of the cytochromefin oxygenic photosynthesis is to act as the terminal electron acceptor in the membrane‐embedded cytochromeb6fcomplex that provides the electron transport connection between the photosystem II and photosystem I reaction centers. Electron transfer through the complex is coupled to proton translocation and generation of a proton electrochemical potential that is utilized to drive the synthesis of ATP through the proton‐motive ATP synthase.

These functions of the cytochromeb6fcomplex are analogous to those of the multisubunit cytochromebc1complex (ubiquinol:cytochromecoxidoreductase) of the mitochondrial respiratory chain and photosynthetic bacteria. Both complexes contain four redox centers with very similar redox and structural properties: a covalently boundc‐type heme in cytochromeforc1, the 2Fe–2S cluster of the Rieske ISP, and the two noncovalently bound hemes of cytochromeb. The structure properties have been defined in 3.0–3.1 Å structures of theb6fcomplex from a thermophilic cyanobacterium and a green alga. These structures also defined a fifth redox prosthetic group, a novel covalently bound heme, tentatively called hemex. With the exception of the extrinsic cytochromesfandc1that, except for the heme‐binding peptide sequence, are completely different, the redox‐active protein subunits of thebc1andb6fcomplexes are structurally similar. For theb6fcomplex, structures at the level of atomic resolution (<2 Å) have also been obtained for the p‐side or lumen‐side extrinsic domains of cytochromefand the Rieske high potential [2Fe–2S] protein, which together constitute approximately 40% of the total mass of the complex.
Cytochromef/Plastocyanin Complex
Authors: Ubbink M
Published: April 2006

In the photosynthetic electron transfer chain in plants, cytochromef, a subunit of the cytochromeb6fcomplex, acts as electron donor for plastocyanin. Plastocyanin is a small soluble protein, which shuttles electrons to photosystem 1. The structure of the short‐lived and weak complex of the soluble domain of cytochromefand plastocyanin has been determined using nuclear magnetic resonance. It shows that the heme iron of cytochromefand the copper ion of plastocyanin are in close proximity, enabling fast electron transfer. The copper ligand His87 is located close to the iron ligand Tyr1, suggesting that electron transfer occurs via the hydrophobic patch of plastocyanin. Electrostatic interactions are also important in the complex. These findings are discussed in the light of studies of the electron transfer kinetics.
Chloroperoxidase
Authors: Sundaramoorthy Munirathinam
Published: April 2006

Chloroperoxidase (CPO) secreted by the marine fungusCaldariomyces fumagocatalyzes the formation of carbon–halide bond between the halide (I–, Br–, or Cl–) and the acceptor substrate. It is the most versatile of the heme (iron porphyrin) enzymes catalyzing four distinct reactionsin vitro, namely, (a) halogenation (haloperoxidase), (b) dehydrogenation (peroxidase), (c) peroxide dismutation (catalase), and (d) mono‐oxygenation (cytochrome P450). CPO is also unique in its structure with a novel tertiary fold, a P450‐like proximal thiolate ligand (Cys29) to heme iron, a peroxidase‐like distal charged residue (Glu183), and extensive glycosylation. This review describes the natural occurrence of CPO, its purification, structural and functional aspects of the native enzyme, enzyme‐intermediates and enzyme‐ligand derivatives characterized by X‐ray crystallography and various spectroscopic methods. The mechanism for the CPO catalytic cycle explaining its diverse functions and the role of the distal residue Glu183 is provided.
Hydroxylamine Oxidoreductase
Authors: Igarashi Noriyuki , Tanaka Nobuo
Published: April 2006

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.
Heme‐Catalases
Authors: Maté Maria J , Murshudov Garib , Bravo Jerónimo , Melik‐Adamyan William , Loewen Peter C , Fita Ignacio
Published: April 2006

The mono‐functional heme‐containing catalases are tetrameric enzymes, ubiquitous in aerobic organisms, specialized in the “catalatic” reaction – the dismutation of hydrogen peroxide to oxygen and water. For these enzymes two well‐defined subgroups can be defined according to the length of their polypeptide subunits of about either 500 or 700 residues, respectively. All the enzymes present a strikingly high structural similarity for about 450 residues that define the “catalase fold” with larger catalases containing an extra “flavodoxin‐like” C‐terminal domain. Catalysis, though centered around the heme iron atom, requires the critical contribution of long and intricate molecular channels.
Rubredoxin
Authors: Meyer Jacques , Moulis Jean‐Marc
Published: April 2006

Rubredoxins are small (45–55 amino acids) proteins containing a single iron ion tetrahedrally coordinated to the sulfur atoms of four cysteine residues occurring in two symmetry‐related Cys‐x‐x‐Cys‐Gly loops. The structure and redox properties of rubredoxins have been analyzed in considerable detail by X‐ray (at atomic resolution) and neutron crystallography, optical spectroscopies, NMR, various other magnetic spectroscopies, and molecular engineering. Variations of the canonical rubredoxin structure include lengthening (Cys‐x‐x‐x‐x‐Cys) or shortening (Cys–Cys) of one of the ligand loops, as well as its integration in larger proteins containing more than one metal site. Rubredoxins are found in a wide range of Archaea and Bacteria, but only exceptionally in Eukarya. They function as electron transfer agents in various redox processes, many of which remain to be fully characterized.
The [2
Fe
–2
S
] Ferredoxins
Authors: Zanetti Giuliana , Binda Claudia , Aliverti Alessandro
Published: April 2006

The 2Fe ferredoxins (Fds) are simple iron–sulfur proteins, containing one 2Fe–2S cluster, that are involved mainly as electron carriers of low oxidation–reduction potential in fundamental metabolic processes. They can be subdivided into three families: class I, plant‐type; class II, adrenodoxin‐type; and class III,
Clostridium
‐type; according to the spacing in the sequence of the cysteinyl residues that bind the iron atoms of the cluster. All the Fds are monomers of 11–14 kDa, except for class III Fds that are dimer, with one cluster per subunit.

The cluster of 2Fe Fds contains two atoms of iron, bridged by two acid‐labile inorganic sulfide atoms, and coordinated to four cysteinyl sulfurs of the polypeptide chain. Fds absorb light in the 300–500 nm visible region, mainly due to sulfur‐Fe
3+
charge‐transfer transitions. The cluster in the oxidized protein contains two antiferromagnetically coupled, high‐spin (S = 5/2) ferric irons and is, therefore, electron paramagnetic resonance (EPR) silent. Upon one‐electron reduction, Fds become paramagnetic.

The three‐dimensional (3D) structure of several 2Fe Fds have been obtained either by X‐ray crystallography or by n
uclear magnetic
resonance (NMR) spectroscopy. The solution structures are very similar to the 3D crystal structures. The protein structure motif characteristic of Fds has been named β‐grasp – a five‐stranded antiparallel β‐sheet with an α‐helix lying on top of the sheet. This central core (β1–β5 and α1) is surrounded by two short β‐strands, an α‐helix (α2), and a short C‐terminal helical turn (α3). Class II Fds have an additional interaction domain. Comparison of the structures of the different proteins reveals conformational differences especially between class I and II ferredoxins. The binuclear iron cluster lies in a solvent‐exposed pocket generated by the loop connecting helix α1 and strand β3 and comprising three of the cysteinyl ligands. This loop is anchored through several hydrogen bonds to different parts of the protein molecule. An extensive survey of the literature on the interactions of several 2Fe Fds with their respective partners is presented.
Ferredoxins Containing Two DifferentFe/SCenters of the Forms [4Fe–4S] and [3Fe–4S]
Authors: Stout Charles D
Published: April 2006

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: April 2006

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.
Methane Monooxygenase Hydroxylase
Authors: Whittington Douglas A , Lippard Stephen J
Published: April 2006

Soluble methane monooxygenase (sMMO) catalyzes the conversion of methane and dioxygen to methanol and water. It is a cytoplasmic system of three proteins produced in methanotrophic bacteria grown under conditions of low copper stress. The best characterized sMMO stems fromMethylococcus capsulatus(Bath). Under physiological conditions inM. capsulatus(Bath), three protein components are required for sMMO activity. These included a 251‐kDa hydroxylase (MMOH), which contains the carboxylate‐bridged, dinuclear iron active site; a 16‐kDa regulatory protein known as protein B (MMOB); and a 38.6‐kDa reductase (MMOR) that contains FAD and a Fe2S2center. MMOH has been characterized by several spectroscopic techniques (UV/vis, X‐ray absorption, Mössbauer, EPR, ENDOR, CD, MCD), which established the nature of the dinuclear iron active site.

The crystal structure of the MMOH component of sMMO fromM. capsulatus(Bath) has been solved in two crystal forms, one of which was refined to a resolution of 1.7 Å. The enzyme is composed of two copies each of three subunits (α2ß2γ2), and all three subunits are almost completely α‐helical. The active site of each α‐subunit contains one dinuclear iron center, housed in a four‐helix bundle. The two iron atoms are octahedrally coordinated by 2 histidine and 4 glutamic acid residues, as well as by a bridging hydroxide ion, a terminal water molecule, and at 4°C, a bridging acetate ion, which is replaced at −160°C with a bridging water molecule. Comparison of the results of the two crystal forms shows one structural difference, namely, the altered side chain conformation of Leu110 at the active site cavity. It is suggested that this residue serves as one component of a hydrophobic gate controlling the access of substrates to and products from the active site. MMOB and MMOR bind to the α‐ and ß‐subunits of MMOH, respectively. The structure of MMOB has been known from NMR. X‐ray structures of reduced MMOH and of DMSO‐soaked MMOH have been determined. During the turnover, Hperoxoand Q intermediate states could be trapped and structures proposed from density functional theory studies.
Iron‐Only Hydrogenases
Authors: Lemon Brian J , Peters John W
Published: April 2006

The Fe‐only hydrogenases, also termed FeFe hydrogenases, catalyze reversible hydrogen oxidation and occur in various microorganisms and a few lower eukaryotes. These enzymes are complex FeS enzymes with unique organometallic biological activity. The Fe‐containing cluster at the active site, termed the H cluster, consists of a complex bridged metal cluster assembly with a [4Fe‐4S] subcluster linked to a 2Fe subcluster containing a unique non‐protein dithiolate linkage and both carbon monoxide and cyanide ligands. Because of the novelty of the active site H cluster, the enzyme has been a very interesting topic for experimental analysis by using a variety of physical methods. This chapter describes methods to probe the activity and electronic structure properties of Fe‐only hydrogenases and the state of the understanding of the mechanistic features of the enzymes based on data compiled to date.
Lactoferrin
Authors: Smith Clyde A
Published: April 2006

Lactoferrin, a member of the transferrin family of proteins, plays an important role as a regulator of the levels of free iron in the body fluids of mammals. The ability to bind Fe3+with high affinity (theKDis approximately 10–20M) and also to retain it to low pH, gives the protein both bacteriostatic and antioxidant properties. A detailed knowledge of the three‐dimensional structure of lactoferrin makes it possible to understand these properties. The lactoferrin molecule is folded into two homologous lobes (N‐ and C‐lobes), each lobe being further divided into two domains. Each lactoferrin molecule is able to bind two metal ions, one in each lobe; the metal binding sites are in the deep cleft formed between the two domains, and metal binding is always associated with the concomitant binding of a carbonate anion. Despite the very high affinity for iron, lactoferrin is nevertheless able to bind a surprisingly wide variety of other metal ions including aluminium and gallium, transition metals such as vanadium, manganese, copper, ruthenium and cadmium, along with the rare earth metals and some actinides. Structural details are known for some of these metal complexes, including Cu2+, Ru3+, Ce4+, and Sm3+, and also for complexes containing an oxalate anion rather than the typical carbonate. It is known that iron binding and release are associated with large conformational changes in which the protein adopts either an open or closed state. Comparisons of structural and functional data on lactoferrins and transferrins now suggest that the key factor comes from cooperative interactions between the two lobes of the molecule, mediated by two α‐helices.
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: April 2006

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.
Nickel–Iron Hydrogenases
Authors: Frey Michel , Fontecilla‐Camps Juan C , Volbeda Anne
Published: April 2006

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.
Peptide Deformylase
Authors: Becker Andreas , Kabsch Wolfgang
Published: April 2006

Peptide deformylase (EC 3.5.1.31) is a mononuclear iron enzyme that cleaves the formyl group of the
N
‐terminal formyl‐methionine residue of nascent polypeptide chains in eubacteria. It is strictly stereospecific for a
L
‐amino acid as the first residue of formyl‐peptide substrates and strongly prefers substrates with at least two or more residues. The native enzyme from

Escherichia coli

is a monomeric protein of 168 amino acid residues that contains one tightly bound Fe
2+
ion. The metal ion is tetrahedrally coordinated by a water molecule and the side chains of residues Cys90, His132, and His136. Similar to thermolysin, the two histidines are part of the HEXXH motif and the glutamate residue is required for enzymatic activity. The native iron form of peptide deformylase is extremely sensitive to oxidative destruction. On substitution of the iron ion by Ni
2+
or Co
2+
the enzyme is insensitive to oxidation and maintains its activity, whereas the Zn
2+
form is nearly inactive.
Diphtheria Toxin Repressor: Metal Ion Mediated Control of Transcription
Authors: Ringe Dagmar , White Andre , Chen Shuyan , Murphy John R
Published: April 2006

The diphtheria toxin repressor is a metal ion–activated DNA‐binding protein that prevents transcription of the diphtheria toxin gene. In its active form the repressor interacts with a semi‐palindromic operator sequence as two noninteracting dimers that recognize overlapping sequences. Recognition of the sequence occurs through two base‐specific interactions. The dimer binds two metal ions per monomer in its active form, only one of which is essential for DNA binding. The mechanism by which activation occurs includes the unraveling of the first turn of the N‐terminal helix in an indirect interaction with the critical metal ion that allows the repressor to interact optimally with the operator sequence of the toxin gene.
Arginase
Authors: Bewley Maria C , Flanagan John M
Published: April 2006

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.
Concanavalin
A
Authors: Kalb (Gilboa) A Joseph , Helliwell John R
Published: April 2006

Concanavalin A is a metalloprotein containing manganese and calcium in a bimetallic metal‐binding site. As isolated from the Jack bean (

Canavalia ensiformis

), the protein binds saccharides such as α‐methyl mannoside and α‐methyl glucoside. Acid treatment produces a demetallized form that does not bind saccharides and that which can be remetallized to produce various metal‐substituted forms, such as (Ni, Ca), (Co, Ca), (Cd, Ca), (Zn, Ca), and (Cd, Cd). Structural studies of the crystal structures of the native, demetallized, and remetallized proteins, as well as its complexes with saccharides, have helped clarify the nature of the interaction between the metal‐binding site and the saccharide‐binding site. The protein has been well‐characterized structurally, namely, at an X‐ray crystallographic resolution of 0.94 Å (Mn, Ca form), by neutron protein crystallography to define the hydration details (at 2.4 Å resolution), by molecular dynamics to better define the protein saccharide recognition, by EPR using the manganese d5 high spin state, and by EXAFS (Zn, Ca form). These structural characterizations include studies at 12 K, 100 K, and room temperature.
Aminopeptidase
P
Authors: Guss J Mitchell , Freeman Hans C
Published: April 2006

Aminopeptidase P is a metalloprotease, which specifically cleaves the N‐terminal residue of a peptide if the second residue is proline. The enzyme is a member of the pita‐bread fold family of metalloenzymes that includes methionine aminopeptidase and prolidase.

Escherichia coli

aminopeptidase P is a tetramer in crystals and in solution. Each subunit has a dinuclear manganese (Mn) centre at its active site. A hydroxide ion that bridges the Mn atoms has been identified as the nucleophile in the enzymatic reaction.
Glutamate Mutase
Authors: Kratky Christoph , Gruber Karl
Published: April 2006

The 5′‐adenosylcobalamin–dependent glutamate mutase catalyzes the reversible and stereospecific equilibration of (S)‐glutamate with (2S,3S)‐3‐methylaspartate through a radical mechanism, whose first step consists of homolysis of the cofactor's cobalt–carbon bond. The enzyme occurs in clostridia, where it catalyzes the first step of the fermentation of glutamate. The protein exists as a heterotetramer of composition ɛ2σ2(B12)2, with each of the two B12cofactor molecules located between an ɛ and a σ peptide. There are two substrate‐binding sites per heterotetramer at a distance of about 6 Å from the B12cofactor. The σ peptide folds as an α/β domain and is very similar to the B12‐binding domains of other B12‐dependent enzymes. The ɛ subunit consists of a (β/α)8‐barrel (TIM‐barrel) domain, whose one end packs against the ‘upper’ face of the B12cofactor, thus forming the active site cavity.
Cobalamin‐Dependent Methionine Synthase
Authors: Gruber Karl , Kratky Christoph
Published: April 2006

The methylcobalamin‐dependent methionine synthase catalyzes the transfer of a methyl group from 5‐methyltetrahydrofolate to homocysteine. This constitutes the terminal step in thede novosynthesis of methionine in eubacteria. In mammals, the enzyme is part of a salvage pathway involved in the conservation of limiting amounts of this essential amino acid. TheEscherichia colienzyme is a modular protein consisting of four distinct regions each with a specific function in the overall catalytic cycle. Crystal structures of two of these modules (the B12‐binding fragment and the C‐terminal activation domain) have been determined.
CO
Dehydrogenase
Authors: Dobbek Holger , Gremer Lothar , Meyer Ortwin , Huber Robert
Published: April 2006

Two principal types of CO dehydrogenases have been discovered, which are distinguished by their metal contents, amino acid sequences, molecular masses, and their sensitivity toward dioxygen.

The CODH from the aerobic eubacterium

Oligotropha carboxidovorans

catalyzes the oxidation of CO with H
2
O, yielding CO
2
, two protons, and two electrons. The enzyme is composed of an 88.7‐kDa molybdoprotein (L), a 30.2‐kDa flavoprotein (M), and a 17.8‐kDa iron–sulfur protein (S) and is organized as a dimer of LMS heterotrimers. The active site of CODH consists of a binuclear heterometal [CuSMo(=O)OH] cluster that is prone to cyanolysis. The cluster is coordinated through interactions of the molybdenum with the dithiolate pyran ring of molybdopterin cytosine dinucleotide and of the copper with Sγ of Cys388; the two metals are bridged by a sulfido‐ligand. A model for the catalytic cycle involves a thiocarbonate‐like intermediate state and includes the transfer of two electrons from Mo through two types of [2Fe–2S]‐clusters to the flavin–adenine dinucleotide cofactor.
Amicyanin and Complexes of Amicyanin with Methylamine Dehydrogenase and Cytochromec551i
Authors: Mathews F Scott
Published: April 2006

Amicyanin is the key component of a soluble periplasmic electron transfer chain in the bacteriumParacoccus denitrificansthat passes electrons from an amine substrate to a terminal oxidase in the periplasmic membrane. It directly and specifically transfers electrons from methylamine dehydrogenase (MADH) to an inducible c‐type cytochrome,c551i. Amicyanin is a 12.5‐kDa monomeric cupredoxin, MADH is a 124‐kDa heterotetramer oxidizing enzyme, andc551iis a 17.5‐kDa monomeric cytochrome. Crystal structures of amicyanin, a binary MADH–amicyanin complex and a ternary MADH–amicyanin–cytochromec551icomplex, are described and correlated with their kinetic and electron transfer properties in solution.
Copper‐Zinc Superoxide Dismutase in Prokaryotes and Eukaryotes
Authors: Bordo Domenico , Pesce Alessandra , Bolognesi Martino , Elena Stroppolo Maria , Falconi Mattia , Desideri Alessandro
Published: April 2006

Cu,Zn superoxide dismutases (SODs) are ubiquitous enzymes catalyzing the conversion of superoxide radical anions into O2and H2O2. In eukaryotes, Cu,Zn SOD is a dimeric protein (2 × 16 kDa); each protomer hosts the binuclear Cu,Zn catalytic center. In prokaryotes, Cu,Zn SODs can be monomeric or dimeric, their quaternary structure differing from that of the eukaryotic homologs. The protein tertiary structure (based on an eight‐stranded antiparallel β‐barrel) is conserved through species. Crystal structures and mutational analysis indicate that Cu,Zn SOD activity is based on a redox cycle, whereby the catalytic Cu(II) species is first reduced (to Cu(I)), and then oxidized (back to Cu(II)) by successive encounters with the substrate. The Zn ion plays a key structural role in maintaining active site structural integrity during the catalytic cycle. Efficient electrostatic steering of the anionic substrate to the active site accounts for the very high (diffusion limited) catalytic turnover displayed by all Cu,Zn SODs. Mutations in human cytoplasmic Cu,Zn SOD have been related to the onset of FALS (familial amyotrophic lateral sclerosis , or Lou Gehring disease), a fatal motoneuron degenerative disease.
Catechol Oxidase
Authors: Eicken Christoph , Gerdemann Carsten , Krebs Bernt
Published: April 2006

Catechol oxidases are ubiquitous plant enzymes with a dinuclear type‐3 copper center. In the wound‐responsive mechanism of the plant, they catalyze the oxidation of a broad range of o‐diphenols to the corresponding o‐quinones coupled with the reduction of oxygen to water. The crystal structures of catechol oxidase from sweet potato in the resting Cu(II)–Cu(II) state, the reduced Cu(I)–Cu(I) form, and in complex with the inhibitor phenylthiourea were analyzed. The catalytic copper center in a central four‐helix bundle is located in a hydrophobic pocket close to the surface. Both metal sites are coordinated by three histidine ligands. His109, ligated to the CuA site, is covalently linked to Cys92 by an unusual thioether bond. On the basis of biochemical, spectroscopic, and structural data, a catalytic mechanism is proposed in which one of the oxygen atoms of the diphenolic substrate binds to CuB of the oxygenated enzyme. There are close structural relationships of catechol oxidase to different hemocyanins.
Binuclear CopperA
Authors: Kroneck Peter MH
Published: April 2006

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.
Vanadium Haloperoxidases
Authors: Wever Ron , Hemrika Wieger
Published: April 2006

This chapter describes the occurrence and the biological function of the vanadium bromoperoxidases and chloroperoxidases. These enzymes that contain vanadate as the prosthetic group catalyze the oxidation of halides to the corresponding hypohalous acids. Purification and molecular characterization of these enzymes is reported and a detailed comparison is made between a bromoperoxidase and a chloroperoxidase, both kinetically as well as structurally. The vanadate‐binding site in haloperoxidases shows an interesting homology with the binding site of phosphate in a large group of phosphatases. Finally, on the basis of mutagenesis studies, a catalytic mechanism is presented for the vanadium chloroperoxidase activity that details the role in catalysis of the amino acid residues in the first coordination sphere of the metal oxide.
The Hydrologic Cycles and Global Circulation
Authors: Oki Taikan
Published: April 2006

The role of hydrological cycles in earth system, the amount of water on the Earth's surface and its distribution in various reserves are first introduced together with the water cycles on the Earth. The concept of mean residence time, water stored in various parts over the Earth surface as various phases, such as glacier, soil moisture, water vapor, and water flux among these reserves, such as precipitation, evaporation, transpiration, and runoff, are briefly explained with their role in global climate system, and their quantitative estimates are presented. Detailed annual water balances over land estimated by land surface models are introduced, as well. Water balance requirements over land, atmosphere, and their coupled system are explained with some application of the concept, and the role of rivers in the global hydrological cycle is quantitatively shown. Finally, the impact of increasing magnitude of anthropogenic activities on global water system and its relationships with global changes are briefly discussed.
Organization and Process
Authors: Kirkby Mike
Published: April 2006

Water, its movement, changes of state, and chemistry, is fundamental to the nature of planet Earth. It is involved in the most important processes near the surface and supports life as we know it. Hydrological sciences potentially address all aspects of water movement and transformation, although with major divisions between hydrology, which is essentially focused on the principle of conservation of mass; hydraulics, based on conservation of momentum (Newton's laws of motion); and meteorology, based on the laws of thermodynamics. This review of processes takes a primarily hydrological viewpoint, concerned with where water is, its pathways, and impacts on other aspects of the environment. A good understanding of these processes is an essential prerequisite to modeling and forecasting the behavior of water, and much of the history of hydrological science reflects changes in our conceptual understanding of how and where water moves. The main theme of this article is the way in which the landscape influences the flow of water, particularly surface hydrology, and how the hydrology in turn influences the form of the landscape.
Fundamental Hydrologic Equations
Authors: Beckie Roger
Published: April 2006

In this article our goal is to present an overview of the fundamental principles that are the basis of most models used in hydrology. We develop the fundamental principles of mass, momentum, and energy conservation and express them in mathematical form. We first outline the general approach that can be used to develop a mathematical statement of a conservation law, using a so‐called Eulerian framework, where we consider volumes fixed in time and space through which material may flow. We then derive the general conservation equations for mass, momentum, and energy for the case of flowing fluids. We next provide examples from hydrology that illustrate the application of the general conservation principles. We begin with relatively straightforward applications of the conservation equations and progress to more complex and less direct applications. Our first and simplest example is the advection–dispersion equation, which is a relatively transparent application of the conservation of mass principle, augmented with a so‐called gradient‐flux model, Fick's law, which describes the dispersion and diffusion of solute mass within the bulk flowing fluid. Next we present the Navier–Stokes equations, which are the conservation of momentum equations for a Newtonian fluid. The next suite of examples involves flow in porous media, which is described by more than one conservation principle applied simultaneously. Our last example is from engineering hydraulics, the Saint Venant equations, which are gross but practical simplifications of the general conservation statements.
Principles of Hydrological Measurements
Authors: Western Andrew W , Grayson Rodger B , Costelloe Justin F
Published: April 2006

This article highlights several key considerations in a successful measurement programme. These are:

The need to have a clear set of objectives or hypotheses to be tested

An understanding of the temporal and spatial variability of the phenomena of interest.

An understanding of the characteristics of the instruments available for measurement, including errors.

Matching of the temporal and spatial characteristics of the measurement with those of the processes of interest.

Considering the trade‐offs inherent in sampling including the number of measurements and accuracy.

Considering a range of practical issues related to setup in the field and the need to check and manage the data as it is collected.

Successful monitoring programs are well designed, well resourced, and analysis will occur during the monitoring program. Timely analysis allows an ongoing review of performance and appropriate modification, which is critical to success.

New and emerging sensor technologies, as well as the ever‐increasing availability of remote sensing information, bode well for the future of hydrological measurement. The synthesis of “smart measurements” with theoretical developments and modeling will yield the greatest advances in the coming years.
Methods of Analyzing Variability
Authors: Gottschalk Lars
Published: April 2006

In an introductory part basic concepts from probability theory, and specifically from the theory of random processes, are introduced as a basis for the characterization of variability of hydrological time series, space processes and time‐space processes. A partial characterization of the random process under study is adopted in accordance with three different schemes:

Characterization by distribution function (one dimensional),

Second moment characterization, and

Karhunen–Loève expansion, that is, a series representation in terms of random variables and deterministic functions of a random process.

The article follows the same division into three major sections. In the first one, distribution functions of frequent use in hydrology are shortly described as well as the flow duration curve. The treatment of second‐order moments includes covariance/correlation functions, spectral functions and semivariograms. They allow establishing the structure of the data in space and time and its scale of variability. They also give the possibility of testing basic hypothesis of homogeneity and stationarity. By means of normalization and standardization, data can be transformed into new data sets owing these properties.

The section on Karhunen–Loève expansion includes harmonic analysis, analysis by wavelets, principal component analysis, and empirical orthogonal functions. The characterization by series representation in its turn assumes homogeneity with respect to the variance–covariance function. It is as such a tool for analyzing spatial‐temporal variability relative to the first‐ and second‐order moments in terms of new sets of common orthogonal random functions.
Co‐Evolution of Climate, Soil and Vegetation
Authors: Berry Sandra L , Farquhar Graham D , Roderick Michael L
Published: April 2006

The myriad of interactions between the vegetation, the soil, the climate, and the air involve transfers of energy and matter between the atmosphere and the lithosphere. In this article, these interactions are investigated mainly from the perspective of the vegetation. Most of the water taken up from the soil by plants is evaporated from the leaves via stomata during the process commonly referred to as transpiration. Transpiration of water is necessary for the uptake of carbon dioxide from the atmosphere for photosynthesis. Through transpiration and photosynthesis, the vegetation links the energy, water, and carbon and other biogeochemical cycles. This linkage provides the backbone to the article. Sections deal with: energy and water limitations to transpiration and plant growth at the catchment scale; the relationship between plant water use and photosynthesis; ecological strategies and temporal variability of water use and volume of soil involved in exchange with the atmosphere; soil water holding capacity and mineral nutrient availability; and catchment scale relationships between vegetation, soil, and climate. In the final sections, the concept of optimality between climate, vegetation, soil, and air is introduced, and the potential application of the optimality approach to hydrology is reviewed.