bluuebunny/crossref_metadata_2025 huggingface dataset:
CytochromecNitrite Reductase
Authors: Einsle Oliver
Published: December 2011

Nitrite (NO2–) is a central intermediate for various metabolic pathways within the biogeochemical nitrogen cycle. In dissimilatory nitrate ammonification, NO2–is reduced to ammonia in a remarkable six‐electron reaction, catalyzed by the multiheme enzyme cytochromecNO2–reductase. The protein is a homodimer with a monomer mass of 58 kDa and five covalently attached heme cofactors, one of which features a free coordination site at the distal axial position of its central iron atom and an unusual and unique lysine ligand on the opposing, proximal axial position. The substrate NO2−binds to this iron atom through the free electron pair on the nitrogen atom and is then reduced consecutively to ammonia, without any detectable release of reaction intermediates or by‐products. In the bacterial cell, many NO2−reductases form a membrane‐associated complex with a small protein, NrfH, which is able to couple the oxidation of menaquinone from within the membrane to electron transfer to the catalytically active NO2−reductase. A proton gradient is generated in a Q‐loop mechanism on NrfH, making NO2−reduction an effective energy metabolism in anaerobic environments.
Heme‐Catalases
Authors: Maté Maria J , Murshudov Garib , Bravo Jerónimo , Melik‐Adamyan William , Loewen Peter C , Fita Ignacio
Published: December 2011

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: December 2011

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.
Ferredoxins Containing One [4Fe–4S] Center
Authors: Fukuyama Keiichi
Published: December 2011

Ferredoxins (Fds) are iron–sulfur proteins that function as electron carriers in diverse metabolic pathways. Generally, Fds are acidic proteins with a low molecular weight and have very low redox potentials. Although historically the name of Fd was given to electron carrier proteins containing iron–sulfur clusters in bacteria, plants and algae, and animals, they differ not only in the foldings of the polypeptide chains but also in the structures of the active centers; the canonical bacterial Fds have one or two [4Fe–4S] (or [3Fe–4S]) centers whereas the plant‐type and animal‐type Fds have one [2Fe–2S] cluster. Bacterial Fds are evolutionally related whether they have one or two [4Fe–4S] (or [3Fe–4S]) clusters, but are distinct from high potential iron–sulfur proteins that also have one [4Fe–4S] cluster. Fds containing one [4Fe–4S] cluster, on which this article is focussed, are one of several distinct classes of bacterial Fds with low redox potentials.
Ferredoxins Containing One [3Fe–4S] Cluster.Desulfovibrio GigasFerredoxinII– Solution Structure
Authors: Moura José JG , Macedo Anjos L , Goodfellow Brian J , Moura Isabel
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification and Molecular Characterization

Metal Content and Cluster Type

Spectroscopy

NMRSolution Structure of NativeD. GigasFdII

Functional Aspects

Structural Cluster Interconversions: Synthesis of Heterometal Clusters

Acknowledgements

Related Articles
High Potential Iron Sulfur Proteins
Authors: Carter Charles W
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purification and Molecular Characterization

Metal Content and Cofactors

Spectroscopy

Activity Tests

X‐Ray Structures of NativeHiPIP

ModelFe4S4Complexes

Functional Aspects

Electron Transfer Mechanisms

Acknowledgments

Related Articles
Naphthalene 1,2‐Dioxygenase
Authors: Ramaswamy S
Published: December 2011

Naphthalene 1,2 dioxygenase (NDO) belongs to the Rieske non‐heme iron oxygenase (RO) family of enzymes. ROs catalyze the first step in the break down of several toxic aromatic compounds and play a key role in global carbon recycling. NDO is an α3β3type enzyme, with one Rieske iron–sulfur cluster and a catalytic mono‐nuclear iron center in every α subunit. They carry outcis‐dihydroxylation, mono‐hydroxylation, sulfoxidation, and demethylation reactions, amongst other reactions on a wide variety of substrates. Yet, the reactions catalyzed by these enzymes are very regio‐ and stereospecific. The article focuses on the structure–function relationship of ROs with NDO as the model.
2,3‐Dihydroxybiphenyl 1,2‐Dioxygenase
Authors: Bolin Jeffrey T , Eltis Lindsay D
Published: December 2011

2,3‐Dihydroxybiphenyl 1,2‐dioxygenase (DHBD) is an Fe2+‐dependent extradiol dioxygenase. DHBD catalyzes the extradiol cleavage of 2,3‐dihydroxybiphenyl (DHB) to 2‐hydroxy‐6‐oxo‐6‐phenylhexa‐2,4‐dienoate (HOPDA) incorporating both atoms of dioxygen into the product HOPDA. DHBDs are found in a range of Gram‐negative and Gram‐positive bacteria that aerobically assimilate biphenyl. Amino acid sequences are available for over 50 bacterial extradiol dioxygenases that are evolutionarily related to DHBDs (i.e. type I enzymes); all are involved in the degradation of aromatic compounds. The type I bacterial enzymes may have large (∼33 kDa) or small (∼21 kDa) monomers. DHBD catalyzes the third reaction of the upperbphpathway, which catabolizes biphenyl to benzoate and 2‐hydroxypentadienoate. This pathway also transforms some polychlorinated biphenyls (PCBs). DHBDs can be best expressed heterologously in pseudomonads likeBurkholderiasp. strain LB400 orPseudomonassp. strain KKS102. Mössbauer and EPR spectroscopies demonstrated the presence of high spin Fe2+in purified active preparations ofPseudomonas putidamt‐2 (C23O).

High‐resolution crystal structures of the active ferrous form of DHBD fromBurkholderiasp. strain LB400 andPseudomonassp. strain KKS102 were determined. These octameric DHBDs have 422 point group symmetry. The monomer has an α + ß fold that may be subdivided into superimposable barrel‐like N‐ and C‐terminal half‐molecules. The active site Fe and the substrate binding sites are located in the cavity of the C‐terminal half. The ferrous Fe is bound by five ligands in square pyramidal geometry. The axial ligand is a conserved histidine, and the basal ligands are a second conserved histidine, a conserved monodentate glutamic acid, and two water molecules. X‐ray structures of DHBD in complex with DHB and 3‐methyl catechol are known for both the ferric and ferrous forms. Spectroscopic, mechanistic, and X‐ray structural studies were used to elaborate a plausible reaction mechanism for DHBDs.
DeacetoxycephalosporinCSynthase
Authors: Andersson Inger , Terwisscha van Scheltinga Anke C , Ranghino Graziella , Valegård Karin
Published: December 2011

Deacetoxycephalosporin C synthase (DAOCS) is a mononuclear ferrous enzyme, which catalyzes the expansion of the five‐membered thiazolidine ring of the penicillin nucleus into the six‐membered dihydrothiazine ring of the cephalosporin nucleus. The reaction requires dioxygen and 2‐oxoglutarate as co‐substrates to create a reactive iron–oxygen intermediate (a ferryl or peroxo compound) from a ferrous iron in the active site of DAOCS. The extended family of 2‐oxoacid‐dependent ferrous enzymes, to which DAOCS belongs, possesses a common jelly roll β‐barrel fold with the ferrous iron ligated by two histidines and a carboxylate. Here we describe the high‐resolution structures of apo‐DAOCS, and of the enzyme in complex with Fe(II) and co‐substrate 2‐oxoglutarate. On the basis of the structures and the quantum‐chemical calculations, a mechanism is proposed whereby the reactive oxidizing species may be stored in a safe form within the enzyme to await the reaction with the penicillin substrate when it is available.
Iron‐Only Hydrogenases
Authors: Lemon Brian J , Peters John W
Published: December 2011

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.
Ferritin
Authors: Theil Elizabeth C
Published: December 2011

The ferritin superfamily of protein nanocages oxidizes ferrous ions to form hydrated ferric oxide nanominerals consisting of thousands of iron and oxygen atoms, in a central, internal cavity; varying amounts of phosphate are incorporated. Maxi‐ferritins, found in all eukaryotes and many bacteria and Archea, have diameters of 10–12 nm, constructed from 24 self‐assembling polypeptide subunits (four‐α‐helix bundles) with cavities of ∼8 nm, while mini‐ferritins in bacteria assemble from 12 subunits, are ∼8 nm in diameter, and have cavities of ∼5 nm. Ferritins function in concentrating iron for protein co‐factor synthesis (heme, FeS, etc.), recovering iron during senescence, and trapping excess iron and oxygen; mini‐ferritins, also called Dps proteins, protect bacterial DNA from chemical/physical damage during stress, in some cases binding the DNA in bacterial “chromatin” structures. There are three types of Fe–protein interaction sites in the nanocages, although when mineralized, most of the iron atoms are in the inorganic phase: 1 – catalytic sites, related by simple DNA coding changes to di‐iron oxygenase co‐factors, that couple two ferrous with oxygen atoms into diferric peroxo and ferric oxy/hydroxo mineral precursors; 2 – nucleation sites on the cavity surface that initiate mineral formation; 3 – gated pores at triple subunit junctions, that control access of reductants and chelators to recover the mineral.

Genetic regulation of ferritin synthesis is unusually complex, depending both on DNA, and, in animals, on mRNA structures that link ferritin to both antioxidant response proteins (DNA regulation) and iron trafficking proteins (mRNA regulation). The lethality of ferritin gene deletion in animals and the recent demonstration that humans absorb ferritin iron from seeds such as soybeans, illustrate the key role played by ferritins in the normal physiology of iron and oxygen. Exploring ferritin interactions with external cellular components that deliver/remove substrates/products, intra‐cage translocation of oxidation products/mineral precursors and reductants, and the potential use of the protein nanocage in materials or pharmacology are directions for the future.
Lactoferrin
Authors: Smith Clyde A
Published: December 2011

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.
Methyl‐CoenzymeMReductase
Authors: Grabarse Wolfgang , Shima Seigo , Mahlert Felix , Duin Evert C , Thauer Rudolf K , Ermler Ulrich
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Metal Content and Cofactors

Protein Production, Purification, Molecular Characterization

Activity Test

Spectroscopy

X‐Ray Structure of InactiveMCR

Functional Aspects

Functional Derivatives

Possible Catalytic Mechanism

Acknowledgements

Related Articles
Diphtheria Toxin Repressor: Metal Ion Mediated Control of Transcription
Authors: Ringe Dagmar , White Andre , Chen Shuyan , Murphy John R
Published: December 2011

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.
AminopeptidaseP
Authors: Guss J Mitchell , Freeman Hans C
Published: December 2011

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 coliaminopeptidase 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: December 2011

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: December 2011

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.
Dissimilatory Nitrate Reductase
Authors: João Romão Maria , Miguel Dias João , Moura Isabel
Published: December 2011

The dissimilatory nitrate reductase (NAP) fromDesulfovibrio desulfuricansATCC 27774 catalyses the reduction of nitrate to nitrite for respiration. It belongs to the DMSO reductase family of molybdoenzymes and contains one single subunit of 755 amino acids with one molybdenum cofactor and one [4Fe–4S] cluster. The Mo atom is coordinated by twocis‐dithiolene groups of two molybdopterin guanine dinucleotides (MGD), by the sulfur atom of Cys140 and by one OH/OH2ligand. One of the MGD cofactors is directly involved in the electron transfer between the molybdenum center and the [4Fe–4S] cluster.
Pseudoazurin
Authors: Adman Elinor T
Published: December 2011

Pseudoazurin is a small blue copper protein isolated from denitrifying bacteria. Its amino acid sequence and molecular structure are distinct from plastocyanin, azurin, and other members of the cupredoxin family. The Type I Cu center responsible for the intense blue color has copper with 2 His, Cys, and Met ligands in a distorted tetrahedral array. Structures of oxidized and reduced forms of the protein show small, but significant differences. Pseudoazurin transfers electrons to and from nitrite reductase. Site‐directed mutagenesis and other techniques have shown that the likely interaction surface is the hydrophobic surface to which the copper atom is closest, surrounded by positively charged residues that interact with negatively charged counterparts on its electron transfer partners.
Amicyanin and Complexes of Amicyanin with Methylamine Dehydrogenase and Cytochromec551i
Authors: Mathews F Scott
Published: December 2011

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.
Prokaryotic Copper Amine Oxidases
Authors: McPherson Michael J , Parsons Mark R , Wilmot Carrie M
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 ofCuAOs

Functional Aspects

Functional Derivatives

Catalytic Mechanism

Related Articles
Galactose Oxidase
Authors: McPherson Michael J , Parsons Mark R , Kate Spooner R , Wilmot Carrie M
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 ofGO

Functional Aspects

Functional Derivatives

Model Compounds

Catalytic Mechanism

Related Articles
Copper‐Zinc Superoxide Dismutase in Prokaryotes and Eukaryotes
Authors: Bordo Domenico , Pesce Alessandra , Bolognesi Martino , Elena Stroppolo Maria , Falconi Mattia , Desideri Alessandro
Published: December 2011

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.
Hemocyanins from Arthropods and Molluscs
Authors: Magnus Karen A
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production, Purifications and Molecular Characterizations

Metal Content and Cofactors

Spectroscopy

Three‐Dimensional Structures of Arthropod and Mollusc Hemocyanins

Functional Aspects

Functional Derivatives

Cooperative Mechanisms

Related Articles
Ascorbate Oxidase
Authors: Messerschmidt Albrecht
Published: December 2011

Ascorbate oxidase (AO) is a multicopper oxidase related to laccase and ceruloplasmin. It catalyzes the four‐electron reduction of dioxygen to water with concomitant one‐electron oxidation of the substrate. The most efficient reducing substrate is l‐ascorbate, but several one‐electron reductants may interact with AO. It occurs in higher plants in both vegetative and reproductive organs in the cytoplasm of the cells. The biological function of AO is still unclear. A very attractive function is its involvement in anti‐oxidative defense. AO has been intensively characterized by spectroscopic, kinetic, electrochemical, and X‐ray crystallographic methods. The amino acid sequences have been determined from several plant sources and fungi. The X‐ray structure of AO from zucchini shows that the monomer of 552 residues is built up by three domains arranged sequentially on the polypeptide chain. The folding of all three domains is of a ß‐barrel type. Each monomer has three disulfide bridges. It contains a mononuclear type 1 copper site in domain 3 and a trinuclear type 2/type 3 copper site between domains 1 and 3. The mononuclear copper site has the four canonical type 1 copper ligands (His, Cys, His, Met) also found in plastocyanin and azurin. The trinuclear copper site has eight histidine ligands (symmetrically supplied by domains 1 and 3) and two oxygen ligands. The type 3 copper pair is bridged by an OH
−
or O
2−
. The remaining copper has two histidine ligands and an OH
−
or H
2
O ligand. The average copper–copper distance in oxidized AO is 3.74 Å. The shortest distance between the type 1 copper center and the trinuclear copper center is 12.2 Å. X‐ray structures of the fully reduced, peroxide and azide forms of AO have been determined. In the fully reduced form, the trinuclear site undergoes strong changes. The bridging oxygen ligand is released and the copper–copper distances increase from an average of 3.7 Å to 5.1 Å for the copper pair and to about 4.2 Å from the paired atoms to the third copper atom. In the peroxide form, the peroxide is bound end‐on to one copper atom of the copper pair while two azide molecules are bound in the same fashion to the same copper atom. Spectroscopic and kinetic studies reveal that the entry site for electrons from the reducing substrate is the mononuclear copper and the dioxygen binding site is the trinuclear copper species. The enzyme acts in a ‘two‐site ping‐pong bi‐bi’ mechanism. A proposal for the catalytic mechanism of AO based on the available data is given. Aspects of intramolecular electron transfer are discussed.
Laccase
Authors: Davies Gideon J , Ducros Valérie
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Metal Content

Activity Tests

Spectroscopy

X‐Ray Structure of Laccase

Functional Aspects

Functional Derivatives

Catalytic Mechanism

Discussion

Acknowledgements

Related Articles
Ceruloplasmin
Authors: Lindley Peter F.
Published: December 2011

Ceruloplasmin is a multi‐copper oxidase that contains most of the copper present in the plasma. It is an acute‐phase reactant that exhibits a two‐ to three‐fold increase over the normal concentration of 300 mg ml−1in adult plasma. However, the precise physiological role(s) of ceruloplasmin has been the subject of intensive debate and it is likely that the enzyme has a multi‐functional role, including iron oxidase activity and oxidation of biogenic amines. The three‐dimensional X‐ray structure of the human enzyme shows that the molecule is composed of six cupredoxin‐type domains arranged in a triangular array. There are six integral copper atoms per molecule (mononuclear sites in domains 2, 4, and 6 and a trinuclear site between domains 1 and 6) and two labile sites with roughly 50% occupancy. Further structural studies on the binding of metal cations by the enzyme have indicated a putative mechanism for ferroxidase activity. Other studies have located the binding sites for an inhibitor (azide) and various substrates [aromatic diamines, biogenic amines, andD‐lysergic acid diethylamide (LSD)]. The binding site of the azide moiety is topologically equivalent to one of the sites reported for ascorbate oxidase. However, there are two distinct binding sites for amine substrates; aromatic diamines bind at the base of domain 4 remote from the mononuclear copper site, whereas the biogenic amine series typified by serotonin, epinephrine, and dopa bind in close vicinity to that site utilized by cations in domain 6 and close to the mononuclear copper.
Structure of the Fourth Metal‐Binding Domain from theMenkes Copper‐TransportingATPase
Authors: Fairbrother Wayne J
Published: December 2011

Functional Class

Occurrence

Biological Function

Amino Acid Sequence Information

Protein Production and Purification

Metal Binding

NMRSolution Structure

Functional Aspects

Note Added in Proof

Related Articles
Vanadium Haloperoxidases
Authors: Wever Ron , Hemrika Wieger
Published: December 2011

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.
Xanthine Oxidoreductase
Authors: Nishino Takeshi , Pai Emil F
Published: December 2011

A single gene product has been identified as responsible for the two catalytic activities, xanthine dehydrogenase, XDH (EC 1.1.1.204), and xanthine oxidase, XO (EC 1.2.3.2). Synthesized as XDH (ultimate electron acceptor NAD+), the protein can be converted to XO (ultimate electron acceptor oxygen) either reversibly by oxidation of cysteine residues or irreversibly by proteolysis. Xanthine oxidoreductase (XOR) is a ubiquitous enzyme; its physiological role is the oxidation of hypoxanthine to xanthine and further to uric acid, althoughin vitrothe enzyme's specificity is rather broad, accepting a large number of purines, pteridines, and aldehydes as substrates. XOR, in contrast to most other hydroxylases, incorporates water‐derived oxygen into its substrate. The electrons are transferred from xanthine to a Mopterin center and from there via two Fe2–S2clusters and FAD to NAD+or oxygen, respectively. The enzyme is the target of the antigout drug allopurinol; it is involved in hyperuricemia and xanthinuria and postulated to participate in postischemic reperfusion injury. Crystal structures have been determined for native and mutant XDHs and XOs from man, cow, rat, andRhodobacter capsulatus. The conformational changes linked to the dehydrogenase/oxidase transition have been identified and interpreted. A structure‐based explanation for the catalytic mechanism is emerging.
Metal ions in cyanobacterial photosystem I
Authors: Saenger Wolfram , Biesiadka Jacek , Loll Bernhard
Published: December 2011

Photosystems I (PSI) and photosystem II (PSII) are large multi‐subunit protein–cofactor complexes located in the photosynthetic thylakoid membrane and acting in series. They are fueled by sunlight, PSII oxidizing water to atmospheric O2, H+, and electrons that are delivered at the lumenal side of the membrane. The electrons are transferred to PSI where their reducing potential is increased sufficiently to finally produce reduced nicotinamide adenine dinucleotide phosphate (NADPH) at oxidized form of nicotinamide adenine dinucleotide phosphate (NADP+) reductase while the H+form a gradient across the membrane that drives adenosine triphosphate (ATP‐)synthetase and both, NADPH and ATP, convert CO2to carbohydrates in the Calvin cycle.

PSI is composed of 12 different protein subunits of which 9 are embedded in the thylakoid membrane and 3 are located on the cytoplasmic (stromal) side of the membrane. Sunlight is absorbed by a large internal antenna composed of 90 chlorophylla(Chla), and the photons are guided to the electron transfer chain (ETC) formed by two symmetry‐related branches where the ‘special pair P 700′ located close to the lumenal side of the membrane is excited and expels an electron to form the cation radical P700+. The electron is guided from P700 to the stromal side along the ETC consisting of pairs of accessory Chla, of the primary electron acceptors (Chla), of the secondary acceptors phylloquinone (PQ), to the terminal acceptors formed by three Fe4S4clusters FX, FA, FB. Since each Chlacoordinates one Mg2+, PSI harbors a plethora of Mg and Fe cations and one structural Ca2+. We describe the coordination of these cations and their function in the photosynthetic process carried out by PSI.
4‐Hydroxybutyryl‐CoADehydratase
Authors: Martins Berta M. , Messerschmidt Albrecht , Friedrich Peter , Zhang Jin , Buckel Wolfgang
Published: December 2011

Dehydratases catalyze the cleavage of a carbon–oxygen bond yielding an unsaturated product via α,β‐elimination of water. The α‐hydrogen (pK ∼ 8) to be removed as proton is activated by an adjacent electron‐withdrawing group, and the hydroxyl group leaves from the β‐position. In contrast, anaerobic organisms possess 2‐ or 4‐hydroxyacyl‐CoA dehydratases that use radicals to lower the pKof the unactivated β‐carbons by 26 units. An example is 4‐hydroxybutyryl‐CoA dehydratase (4‐BUDH) fromClostridium aminobutyricumthat interconverts 4‐hydroxybutyryl‐CoA to crotonyl‐CoA. 4‐BUDH is functional as a homotetramer with two active sites per dimer and displays a distinctive active site architecture with the [4Fe–4S]2+cluster, coordinated by three cysteine and one histidine residues, located 7 Å from theRe‐side of the flavin adenine dinucleotide (FAD). Albeit requiring the cluster and an oxidized FAD for catalysis, the overall reaction occurs with no net redox change. The unexpected structural relation of 4‐BUDH with medium chain acyl‐CoA dehydrogenases suggests a radical‐based mechanism for both flavoproteins. The biochemical and structural characterization of 4‐BUDH is an important step toward a detailed study of the structural bases how enzymes regulate the generation and reactivity of radical species at a molecular level, which is a fundamental but still poorly understood problem.
Human Ferrochelatase
Authors: Lanzilotta William N , Dailey Harry A
Published: December 2011

Ferrochelatase catalyzes the terminal step of heme biosynthesis, the insertion of ferrous iron into protoporphyrin IX to form heme. The mammalian enzyme is a homodimer with a total molecular weight of 83 000 and is associated with the matrix side of the inner mitochondrial membrane. Each subunit contains a [2Fe–2S] cluster whose coordination and spectral properties are unlike any other currently characterized [2Fe–2S] cluster. The crystal structure of the human enzyme both with and without porphyrin substrate‐bound is presented and discussed. The enzyme without substrate‐bound possesses an open mouth for an active site with the two lips of the mouth being responsible for interaction with the membrane. The enzyme with bound porphyrin has a closed mouth that results in a hand‐in‐glove fit with the porphyrin substrate.
Flavodiiron Proteins: Nitric Oxide and/or Oxygen Reductases
Authors: Vicente João B , Carrondo Maria Arménia , Teixeira Miguel , Frazão Carlos
Published: December 2011

Flavodiiron proteins (FDPs) have been isolated from and identified in genomes of bacteria, archaea, and a restricted group of pathogenic protozoa, mostly anaerobes or microaerophiles. The current knowledge on this protein family suggests alternative or complementary roles in nitric oxide (NO) and/or oxygen detoxification in anaerobes. These enzymes couple substrate (NO, O2) reduction to the oxidation of NAD(P)H or F420H2through electron transfer chains with varying complexity. The first crystallographic structure of an FDP, theDesulfovibrio gigasrubredoxin:oxygen oxidoreductase (Dg_ROO), revealed the structural prototype of this family and the identification of common amino acid sequence motifs. The common functional unit of the FDP family is a ‘head‐to‐tail’ homodimer, each monomer comprising two structural domains: an N‐terminal metallo‐β‐lactamase‐like domain, where a nonheme diiron center is embedded (being the active site of NO/O2reduction), and a C‐terminal flavodoxin‐like domain, harboring a flavin mononucleotide (FMN) moiety. The homodimer ‘head‐to‐tail’ arrangement places the diiron from each monomer in close proximity with the FMN from its opposing monomer, allowing efficient electron transfer between cofactors, otherwise impaired by their large distance within the same monomer.

Herein are summarized structural and functional features of FDPs from several organisms, which provide clues to an understanding of their role in microbial nitrosative and/or oxidative stress resistance.
Glutamate CarboxypeptidaseII
Authors: Mesters Jeroen R , Hilgenfeld Rolf
Published: December 2011

Glutamate carboxypeptidase II (GCP II) is a homodimeric, dinuclear zinc carboxypeptidase that catalyzes the cleavage of two endogenous substrates carryingL‐glutamate at the C‐terminal P1′ position, namelyN‐acetyl‐L‐aspartyl‐α‐L‐glutamate (α‐NAAG) and folylpoly‐γ‐L‐glutamate (folylpolyglutamate). Former synonyms for GCP II, a type‐II membrane glycoprotein that belongs to the transferrin receptor family of proteins, include prostate‐specific membrane antigen (PSMA), folylpoly‐γ‐glutamate carboxypeptidase (FGCP), andN‐acetylated α‐linked acidic dipeptidase (NAALADase). GCP II predominantly occurs in nearly all types of glial cells and is drastically overproduced in endothelial cells of tumor‐associated neovasculature and in prostate cancer tissue. The particular role of PSMA, a folylpolyglutamate hydrolase, in prostate cancer is poorly understood. In the brain, GCP II catalyzes the cleavage of the abundant neuropeptide α‐NAAG that acts as an agonist for the metabotropic (i.e. G‐protein‐coupled) glutamate receptor‐3 (mGluR3), and as a mixed agonist/antagonist forN‐methyl‐D‐aspartate (NMDA) receptors. The liberatedL‐glutamate acts as a downstream neurotransmitter that is excitotoxic at high concentrations, harming retina and brain. Accordingly, inhibitory compounds of GCP II have been shown to provide neuroprotection. In addition, they may prove useful, through the binding to PSMA, for the imaging and possible treatment of certain forms of cancer.
Nitrogenase: Recent Advances
Authors: Andrade Susana LA , Hu Yilin , Ribbe Markus W , Einsle Oliver
Published: December 2011

Nitrogenase catalyzes the reductive fixation of nitrogen from atmospheric N2for biological syntheses, and as such it constitutes the only enzyme known to be able to cleave the highly stable triple bond of the dinitrogen molecule. Structures are known of both component proteins of nitrogenase, the enzymatically active MoFe protein and its electron donor, the Fe protein. In spite of a wealth of biochemical and biophysical data on nitrogenase, the mechanistic details of its action remain poorly understood. This article provides an update on recent results in nitrogenase research, including the discovery of a central, light atom in the center of the FeMo cofactor, studies on substrate binding to the cofactor in mutant proteins, and novel aspects of complex formation between both component proteins. Particular emphasis is given to the significant progress made in understanding the biosynthesis of the complex metal clusters of the MoFe protein, the P‐cluster and the FeMo cofactor.
Ribonucleotide Reductase: Recent Advances
Authors: Stubbe JoAnne , Cotruvo Joseph A
Published: December 2011

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides and play an essential role in nucleic acid metabolism in all organisms. RNRs have been divided into three classes. They share a structurally homologous subunit where the reduction occurs, with the chemistry being initiated by thiyl radical‐mediated abstraction of the nucleotide's 3′‐hydrogen atom. The classification of RNRs is based on the different strategies used to generate the transient thiyl radical. The class Ia and Ib RNRs use a diferric‐tyrosyl radical cofactor, the class II RNRs use adenosylcobalamin, and the class III RNRs use a glycyl radical generated by a [4Fe4S]1+cluster andS‐adenosylmethionine. This article focuses on the recent advances in our understanding of thein vitroandin vivomechanisms of formation of the metallocofactors in the class I RNRs inE. coliandS. cerevisiae. The discovery of a new class of RNR, class Ic, whose active cofactor is proposed to be an MnIVFeIIIcluster, and a summary of recent insights into the chemistry of the novel cofactor are also described. Finally, the current understanding of the unprecedented role of the metallocofactor in radical propagation over 35 Å in the class Ia—and presumably class Ib and Ic—RNRs is presented.
TheMre11 Nuclease Complex
Authors: Hopfner Karl‐Peter , Bemeleit Derk , Lammens Katja
Published: December 2011

The repair of DNA double‐strand breaks (DSBs) is necessary to maintain genome stability and prevent cell aberration and cancer development. Meiotic recombination 11 (Mre11) and radiation sensitivity 50 (Rad50) form an evolutionary conserved complex (denoted Mre11 complex) that is a key factor in the detection, repair, and signaling of DSBs. The Mre11 complex possesses ATP‐stimulated DNA binding, DNA endo‐ and exonuclease activities as well as DNA cross‐linking functions. The Mre11 complex is a primary sensor for DNA DSBs and is involved in many aspects of the repair of and cellular response to DNA DSBs. Its activity is controlled by at least three different metal binding sites, a manganese‐dependent nuclease (Mre11 phosphodiesterase domain), a magnesium‐dependent ATPase (Rad50 ABC ATPase domain), and a zinc‐mediated DNA tethering function, located at the apex of a long Rad50 coiled‐coil domain. Although the mechanism remains to be shown, current structural and functional data indicate that the Mre11 complex is an ATP‐dependent cross‐linker and a processing factor for DNA ends.
Acetylene Hydratase
Authors: Seiffert Grazyna B , Abt Dietmar , tenBrink Felix , Fischer David , Einsle Oliver , Kroneck Peter MH
Published: December 2011

The tungsten‐iron‐sulfur enzyme acetylene hydratase is a rather unique enzyme within the class of tungsten/molybdenum enzymes in the sense that it catalyzes a nonredox reaction, the addition of one molecule of water to the CC bond of acetylene to form acetaldehyde. Its crystal structure (1.26 Å) reveals a close to octahedral, or trigonalantiprismatic tungsten center, which binds a water molecule that gets activated by an adjacent aspartate residue such that it can attack an acetylene molecule bound in a distinct, hydrophobic pocket. This requires a strong shift of pKaof the aspartate, caused by a nearby low‐potential [4Fe–4S] cluster. To gain access to this novel W‐Asp‐active site, the protein evolved a new substrate channel distant from where it is found in other molybdenum and tungsten enzymes.
VAP1—Snake Venom Homolog of MammalianADAMs
Authors: Takeda Soichi
Published: December 2011

Vascular‐apoptosis‐inducing protein‐1 (VAP1) is a zinc endopeptidase from western diamondback snakeCrotalus atroxvenom. VAP1 possesses a metalloproteinase/disintegrin/cysteine‐rich (MDC) domain that bears the typical domain architecture of the adamalysin/reprolysin/ADAM (a disintegrin and metalloproteinase) family of proteins. Mammalian ADAM proteinases are unique in that they have both proteolytic and adhesive properties. Additionally, as cell‐surface proteins, they constitute a major class of membrane‐anchored sheddases and participate in the processing of cell‐surface‐protein ectodomains, including the latent forms of growth factors, cytokines, and receptors. The crystal structures of VAP1 reveal a C‐shaped MDC domain architecture and a potential protein–protein interaction site in the C domain that faces the catalytic site in the M domain. The structures of VAP1 and related proteins suggest that there is interplay between proteolytic and adhesive functions in the proteinases of the adamalysin/reprolysin/ADAM family.
The
Mgt
E
Mg
2+
Transporter
Authors: Maguire Michael E
Published: December 2011

The MgtE class of Mg
2+
ion transporter is widespread in the bacteria, with over 50% of current genomic sequences and most marine metagenome sequences exhibiting a homolog. MgtE is the primary provider of cytosolic Mg
2+
in those organisms that carry it. MgtE homologs are widespread in the metazoa and fungi (SLC41 family) but apparently absent in the plants. In bacteria, MgtE functions as a Mg
2+
influx system, while in eukaryotes specific MgtE proteins may function as either influx or efflux systems. Despite their ubiquity, virtually nothing is known about the physiological role of MgtE. Bacterial MgtE proteins are homodimers, with the entire soluble domain at the N terminus and the entire membrane domain at the C terminus. A recent crystal structure of

Thermus thermophilus

MgtE putatively in the closed form shows that the membrane domain consists of 5 transmembrane helices, each at a substantial angle to the plane of the membrane, giving 10 transmembrane helices in the dimer. The pore is formed primarily by transmembrane segments 2 and 5. Each membrane domain is connected to the soluble domain by a single α‐helix orthogonal to the membrane. Attached to this ‘connecting helix’ is a soluble domain containing a superhelical bundle of 10 α‐helices (‘N domain’) followed by duplicated tandem cystathionine β‐synthase‐like motifs, which end in the ‘connecting helix.’ The N domain has structural homology to the FliG protein of the flagellar motor. It is not clear how Mg
2+
is recognized and selected. The crystal structure also contains several sites for bound Mg
2+
ions, one within the pore. Two Mg
2+
sites per monomer connect the ‘connecting helice’ and CBS domain to the membrane domain, while two additional sites per monomer connect the CBS‐ and N domains. The structure of the soluble domain with and without Mg
2+
has also been solved. The absence of Mg
2+
does not alter the structure of the N domain significantly, but the structure of the tandem cystathionine β‐synthase domains within each monomer does change to some extent. The largest change due to the absence of Mg
2+
is that the entire cystathionine β‐synthase domain rotates and slightly twists 120° from the N domain. It is not clear if this rotation is part of the mechanism by which the pore opens and closes. Presumably, the bound Mg
2+
ions in the soluble domain play a role in sensing Mg
2+
, and their dissociation could allow domain movement and lead to opening of the pore.
Mitochondrial Respiratory
C
omplex
II
Authors: Bartlam Mark , Sun Fei , Rao Zihe
Published: December 2011

The mitochondrial respiratory Complex II, or succinate : ubiquinone oxidoreductase (SQR), is an integral membrane protein complex in both the tricarboxylic acid cycle (Krebs cycle) and aerobic respiration. To date, X‐ray crystal structures of mitochondrial respiratory Complex II have been reported from porcine heart and from chicken, as well as the structures of a number of related bacterial SQR or quinol : fumarate oxidoreductase (QFR) structures. Complex II comprises of two hydrophilic proteins (flavoprotein (Fp) and iron–sulfur protein (Ip)) and two transmembrane proteins (CybL and CybS), as well as prosthetic groups required for electron transfer from succinate to ubiquinone. A proximal ubiquinone site (Qp) is located on the matrix side of the protein complex. Inhibitor‐bound structures using 3‐nitropropionate (NPA), 2‐thenoyltrifluoroacetone (TTFA), and carboxin provide further functional details for Complex II. NPA, a succinate analog, confirms the location of the succinate binding site. TTFA, a classical inhibitor for the ubiquinone reduction of Complex II that works by occupying its ubiquinone binding sites, confirms the location of the Qp site in both porcine heart and chicken structures. The available Complex II structures provide models for studying the mitochondrial respiratory system and human mitochondrial diseases related to mutations in this complex.