bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytochromec553
Authors: Nakagawa Atsushi 
Published: December 2011

AbstractCytochromec553in sulfate‐reducing bacteria,Desulfovibrio vulgaris, receives electrons from formate dehydrogenase and lactate dehydrogenase, and then transfers them to cytochromec3. Cytochromec553is a monohemec‐type cytochrome with an absorption band at 553 nm in the reduced form and is the smallestc‐type cytochrome with a molecular weight of 9000. Its three‐dimensional structure has been determined by both x‐ray crystallography and NMR.
Cytochromec6
Authors: Reuter Wolfgang , Wiegand Georg 
Published: December 2011

AbstractCytochromec6, or its functional analog copper protein plastocyanin, mediates the intrathylakoidal photosynthetic electron transfer from the always dimeric cytochromeb6fcomplex to the monomeric and/or trimeric Photosystem I (PS I) complex. The high‐potential monoheme protein belongs to the omnipresent cytochromecfamily 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 cytochromec6from various organisms, the real molecular events that occur during its reduction by cytochromeb6fand its oxidation by the reaction center of PS I are presently uncertain. In addition, the specific role of cytochromec6within the hydrogen metabolism in an anaerobic environment is in the focus of interest. However, the presentation of established information about cytochromec6is 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: December 2011

Abstract

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.
Photosynthetic Reaction Centers of Purple Bacteria
Authors: Lancaster C Roy D , Michel Hartmut 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification, and Molecular CharacterizationMetal Content and CofactorsSpectroscopyX‐Ray Structures ofRCsfrom Purple BacteriaFunctional AspectsFunctional DerivativesInter‐ and Intramolecular Electron and Proton Transfer and Catalytic MechanismRelevance to PhotosystemIIRelated Articles
Cytochromec554
Authors: Iverson Tina M , Hendrich Michael P , Arciero David M , Hooper Alan B , Rees Douglas C 
Published: December 2011

AbstractCytochrome c554(cyt c554) is a tetra‐hemec‐type cytochrome that participates in the nitrification pathway ofNitrosomonas europaea. In this process, cyt c554functions as the electron acceptor from the enzyme hydroxylamine oxidoreductase that catalyzes the oxidation of hydroxylamine to nitrite. Cyt c554is a predominantly α‐helical protein with four covalently attached hemes. The four hemes are arranged in two pairs, such that the planes of the porphyrin rings are nearly parallel and overlapping at the edges. This type of heme‐stacking has been observed in two other nitrogen cycle proteins: hydroxylamine oxidoreductase and cytochrome c nitrite reductase, an enzyme that catalyzes the reduction of nitrite to ammonia. The relatively unusual spectral properties of cyt c554may reflect interactions between these pairs of stacked hemes.
Nine‐Heme Cytochrome

c
Authors: Arménia Carrondo Maria , Soares Cláudio M , Matias Pedro M 
Published: December 2011

Abstract

Nine heme cytochrome c (9Hcc) is a monomeric multi‐heme cytochrome c found in the sulfate‐reducing bacteria of

Desulfovibrio desulfuricans

(Dd) ATCC 27774 and

Desulfovibrio desulfuricans

Essex 6. The polypeptide chain comprises 296 residues and wraps around nine hemes of type‐c that bind the polypeptide chain through thioether bridges to cysteine residues. This represents the first known structure of a multi‐heme cytochrome where copies of a tetra‐heme cytochrome
c
3
‐like fold are present in the same polypeptide chain.

The high homology between 9Hcc and the C‐terminal region of

Desulfovibrio vulgaris

Hildenborough (DvH) Hmc, as well as the presence of the
9Hcc
gene within an operon similar to that of the DvH Hmc, strongly support the proposal that 9Hcc is the high‐molecular‐weight cytochrome of Dd. Several
in vitro
studies, as well as our crystallographic and modeling studies suggest that cytochrome
c
3
is the mediator between the [NiFe] hydrogenase and 9Hcc in Dd.
Cytochromef/Plastocyanin Complex
Authors: Ubbink M 
Published: December 2011

AbstractIn 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.
Horseradish Peroxidase
Authors: Gajhede Michael 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsSpectroscopyX‐ray Structure of NativeHRPCFunctional AspectsFunctional DerivativesX‐ray Structure ofHRPC:Benzhydroxamic Acid ComplexX‐ray Structure ofHRPC:Ferulic Acid ComplexX‐ray Structure of TernaryHRPC:FA:CN−ComplexCatalytic MechanismAcknowledgementsRelated Articles
Myeloperoxidase
Authors: Fenna Roger E 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestSpectroscopyX‐Ray Crystal Structure ofMPOFunctional AspectsFunctional DerivativesCatalytic MechanismRelated Articles
Arthromyces Peroxidase
Authors: Fukuyama Keiichi 
Published: December 2011

AbstractHeme peroxidase catalyzes the oxidation of a variety of compounds by utilizing hydrogen peroxide. The resting peroxidase reacts with hydrogen peroxide to yield an intermediate compound I, which is reduced to the resting stateviathe second intermediate compound II, by the use of reducing substrates. The reducing substrates include naturally occurring organic compounds such as phenols and ascorbic acid, diagnostic reagents such as luminol and 4‐amino‐antipyrine, as well as inorganic compounds such as halide ions, ferrocyanide, and isothiocyanate.Arthromycesperoxidase is a class II peroxidase in the plant peroxidase superfamily, and has the characteristics of giving extraordinarily high chemiluminescence in the oxidation of luminol.
Chloroperoxidase
Authors: Sundaramoorthy Munirathinam 
Published: December 2011

AbstractChloroperoxidase (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.
Prostaglandin EndoperoxideH2Synthases‐1 and ‐2
Authors: Michael Garavito R 
Published: December 2011

AbstractThe prostaglandin endoperoxide H2synthase (PGHS) isozymes 1 and 2 are membrane bound, heme‐dependent enzymes that catalyze the committed step in the conversion of polyunsaturated fatty acids to prostanoids and thromboxanes. The PGHS isozymes, which are also known as cyclooxygenases, produce prostaglandin H2in two sequential enzymatic steps – a bis‐oxygenase (cyclooxygenase) reaction generates prostaglandin G2from arachidonic acid and a hydroperoxidase reaction creates the final product, prostaglandin H2. The PGHS isozymes are also the primary targets of nonsteroidal anti‐inflammatory drugs (NSAIDs), such as aspirin and ibuprofen, and recent pharmacological research efforts have led to the development of isoform selective drugs like Celebrex® and Vioxx®. In this chapter, we discuss the biochemistry, enzymology, and the structural biology of the PGHS isozymes and their relevance to prostanoid physiology and NSAID pharmacology.
CytochromeP450
Authors: Li Huiying 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestSpectroscopyX‐Ray Structure of CytochromesP450Structures of Functional IntermediateStructure‐Based Sequence AlignmentFunctional AspectsRelated Articles
Inducible Nitric Oxide Synthase
Authors: Rosenfeld Robin J , Tainer John A , Getzoff Elizabeth D 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification, and Molecular CharacterizationActivity TestsMetal Content and CofactorsSpectroscopyX‐Ray StructuresFunctional AspectsFunctional DerivativesIntramolecular Electron Transfer and Catalytic MechanismAcknowledgementsRelated Articles
Endothelial Nitric Oxide Synthase
Authors: Raman C S 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestSpectroscopyX‐Ray StructureInterdomain Electron‐Transfer and CatalysisRelated Articles
Heme Oxygenase
Authors: Schuller David J 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestSpectroscopyX‐Ray Structures of MammalianHO‐1 with HemeFunctional AspectsCatalytic MechanismRelated Articles
Bacterial CytochromecOxidase
Authors: Kannt Aimo , Michel Hartmut 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production and PurificationMetal Content and CofactorsActivity TestSpectroscopyX‐Ray Structure of Bacterial CytochromecOxidaseCrystallizationOverall Description of the StructureFunctional AspectsSummaryRelated Articles
Mitochondrial Cytochrome

c

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

Abstract

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

a
3

O
2
and Fe

a
3

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

Abstractba3‐Cytochromecoxidase fromThermus thermophilusis a terminal enzyme of respiration that catalyzes the reduction of dioxygen to water. It is produced at low oxygen tension and is one of the most divergent members of the heme–copper oxidase superfamily.ba3‐Oxidase has been isolated fromT. thermophilusmembranes, purified and characterized using several biochemical and biophysical techniques. Its crystal structure has been solved at high resolution. The current review summarizes the results on structure and function relationship ofba3‐oxidase that have been elucidated during the last decade.
Hydroxylamine Oxidoreductase
Authors: Igarashi Noriyuki , Tanaka Nobuo 
Published: December 2011

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

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification, and Molecular CharacterizationMetal Content and CofactorsActivity AssaySpectroscopyCrystallography and Structure of NativeSiRHPFunctional AspectsRelationship between Structure and Redox States: Implications for CatalysisConclusionsNote Added in ProofAcknowledgments
FeSRieske Center
Authors: Link Thomas A 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationBiosynthesisProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestSpectroscopyX‐Ray StructureFunctional AspectsFunctional DerivativesCatalytic MechanismRelated Articles
Ferredoxins Containing Two DifferentFe/SCenters of the Forms [4Fe–4S] and [3Fe–4S]
Authors: Stout Charles D 
Published: December 2011

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

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

Abstract

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

Desulfovibrio vulgaris

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

Rhodobacter capsulatus

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

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

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

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid and Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestSpectroscopyX‐Ray Structure ofE. ColiR2X‐Ray Structure ofE. ColiR1Crystal Structure ofS. TyphimuriumR2Crystal Structure of MouseR2Functional AspectsFunctional DerivativesTyrosyl Radical SiteOxidation of Tyrosine 122 to a Radical SpeciesCatalytic MechanismRelated Articles
Δ9Stearoyl‐Acyl Carrier Protein Desaturase
Authors: Lindqvist Ylva 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestSpectroscopyX‐Ray Structure of Δ9Stearoyl‐Acyl Carrier Protein DesaturaseFunctional AspectsThe Catalytic MechanismAcknowledgementsRelated Articles
Cytochromeb1– Bacterioferritin
Authors: Frolow Felix , Kalb(Gilboa) Aaron Joseph 
Published: December 2011

AbstractCytochrome b1, also known as bacterioferritin, has been isolated fromEscherichia coli, as well as many other bacteria. This large 400‐kD protein is composed of 24 identical subunits arranged in a shell of cubic (432) symmetry and contains at least three distinct forms of iron:12 heme irons coordinated by pairs of methionine sulfurs from contiguous twofold symmetry related subunits48 iron atoms, two in each subunit, occupying aquasi‐symmetric binuclear metal‐binding siteseveral thousand bulk iron atoms that may be deposited as a microcrystalline polymeric mineral in the hollow interior of the ferritin‐like protein shell.