bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytochrome

c

Nitrite Reductase
Authors: Einsle Oliver 
Published: April 2006

Abstract

Nitrite (NO
2
–
) is a central intermediate for various metabolic pathways within the biogeochemical nitrogen cycle. In dissimilatory nitrate ammonification, NO
2
–
is reduced to ammonia in a remarkable six‐electron reaction, catalyzed by the multiheme enzyme cytochrome
c
NO
2
–
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 NO
2
−
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 NO
2
−
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 NO
2
−
reductase. A proton gradient is generated in a Q‐loop mechanism on NrfH, making NO
2
−
reduction an effective energy metabolism in anaerobic environments.
Ferredoxins Containing One [4Fe–4S] Center
Authors: Fukuyama Keiichi 
Published: April 2006

AbstractFerredoxins (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.
2,3‐Dihydroxybiphenyl 1,2‐Dioxygenase
Authors: Bolin Jeffrey T , Eltis Lindsay D 
Published: April 2006

Abstract

2,3‐Dihydroxybiphenyl 1,2‐dioxygenase (DHBD) is an Fe
2+
‐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 upper
bph
pathway, which catabolizes biphenyl to benzoate and 2‐hydroxypentadienoate. This pathway also transforms some polychlorinated biphenyls (PCBs). DHBDs can be best expressed heterologously in pseudomonads like
Burkholderia
sp. strain LB400 or
Pseudomonas
sp. strain KKS102. Mössbauer and EPR spectroscopies demonstrated the presence of high spin Fe
2+
in purified active preparations of
Pseudomonas putida
mt‐2 (C23O).

High‐resolution crystal structures of the active ferrous form of DHBD from
Burkholderia
sp. strain LB400 and
Pseudomonas
sp. 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.
Hemerythrin
Authors: Stenkamp Ronald E 
Published: April 2006

AbstractHemerythrin is a non‐heme iron protein that serves as an oxygen transfer or storage protein in several marine invertebrate phyla (sipunculids, brachiopods, priapulids and annelids). Each protein subunit (13 500 kD) binds two iron atoms by histidine, aspartic acid, and glutamic acid side‐chains. The protein carboxylates and a μ‐oxygen atom bridge the iron atoms in a prototypic FeOFe complex that has been extensively studied. One iron binds exogenous ligands including dioxygen and small anions. The protein functions by reversibly adding dioxygen to a deoxy form containing ferrous iron to produce an oxy form containing ferric iron and a peroxo anion.
Aldehyde Oxidoreductase (
MOP
)
Authors: João Romão Maria , Moura José JG 
Published: April 2006

Abstract

The aldehyde oxido‐reductase from

Desulfovibrio gigas

(MOP) is a member of the xanthine oxidase family but simpler since it lacks the flavin–adenine dinucleotide (FAD) domain. It is composed of a single polypeptide chain of 907 amino acids and contains one molybdenum atom bound to a molybdopterin cytosine dinucleotide (MCD) cofactor, as well as two spectroscopically distinguishable [2Fe2S] clusters involved in electron transfer. The Mo atom is pentacoordinated by the two sulfurs of the
cis
‐dithiolene group of the molybdopterin, plus two oxo and one hydroxyl/water ligand. It hydroxylates a wide range of aldehydes with little specificity but its physiological role is not totally clear.
Sulfite Oxidase
Authors: Kisker Caroline 
Published: April 2006

AbstractSulfite oxidase catalyzes the physiologically vital oxidation of sulfite to sulfate, the terminal reaction in the oxidative degradation of the sulfur‐containing amino acids, cysteine and methionine. It belongs to the molybdenum cofactor (Moco)‐containing family of enzymes that are characterized by the presence of a mononuclear Mo atom coordinated to the sulfur atoms of a pterin derivative, named molybdopterin. The homodimeric sulfite oxidase is located in the mitochondrial intermembrane space and each subunit contains a larger Moco‐containing domain and a smaller heme‐containing domain. Oxidation of sulfite to sulfate occurs at the molybdenum center with concomitant reduction of Mo(VI) to Mo(IV). Two electrons are singly transferred to theb5heme of the enzyme and from there to cytochromec. Sulfite oxidase deficiency results from defects either in the genes encoding proteins involved in molybdenum cofactor biosynthesis or in the sulfite oxidase gene itself. Several point mutations in the sulfite oxidase gene have been identified in patients with this disease worldwide. The crystal structure of wild‐type chicken sulfite oxidase provides the first atomic model for this enzyme and suggests possible reasons for how these substitutions interfere with catalysis or substrate binding.
Eukaryotic Copper Amine Oxidases
Authors: Wertz Diana L , Klinman Judith P 
Published: April 2006

AbstractCopper amine oxidases contain the covalently bound quinone cofactor, topaquinone, in addition to an active site copper. These proteins are widely distributed among both prokaryotes and eukaryotes and have been characterized with regard to kinetic and structural properties. The function of the eukaryotic proteins is only now beginning to be understood with the hypothesis ranging from a role in cell–cell adhesion to a role in insulin signaling.
Ascorbate Oxidase
Authors: Messerschmidt Albrecht 
Published: April 2006

Abstract

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.
Ceruloplasmin
Authors: Lindley Peter F. 
Published: April 2006

Abstract

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
−1
in 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, and
D
‐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.
Yeast Copper Metallothionein
Authors: Peterson Cynthia W 
Published: April 2006

AbstractThe first structure of yeast copper metallothionein (1) was determined from solution NMR data using experimental NOEs and dihedral angle constraints along with specific metal to Cys connectivities derived for the isomorphic Ag(I) substituted Cu(I) yeast MT. In solution, both MTs bind seven moles of Cu(I) or Ag(I) ions, respectively, in a single cluster embedded in a cleft between two large parallel protein loops with only the metals on the open side of the cleft exposed to the solvent.It is reassuring to see the precision of the earlier solution structure compared to the recently published crystal structure (2) of a yeast copper thionein construct lacking the first 4 and last 13 residues of the intact protein. All of the crystal metal–Cys connectivities are identical to the previous solution structure, with the additional verification of the earlier postulated third Cys ligand to metal VI. The only difference is that the truncated, crystallized CuMT protein binds an eighth Cu(I) ion, labeled Cu39. (Note error in (2) where the “copper ion missing in solution structure” is misidentified as Cu44). Considering the fact that two of the three coordinating cysteines for Cu39 in (2) come from the N terminus, it is conceivable that cutting off four residues from this end enables an eighth metal to bind. Unfortunately, no solution study of the Cu(I) binding stoichiometry to this truncated form of the protein was reported. Naturally, the important structure is the structure of the native, full‐length yeast MT. We, therefore, recommend that caution be exercised before drawing any conclusions about the native protein structure on the basis of the crystal structure on the truncated yeast MT construct.
Flood Early Warning Systems for Hydrological (Sub) Catchments
Authors: Werner Micha Guido Franciscus , Schellekens Jaap , Kwadijk Jacob Cornelis Jan 
Published: April 2006

AbstractProvision of early warning is an effective strategy in reducing flood damage and loss of life due to flooding. Flood forecasting and warning systems are important instruments in supporting relevant authorities issuing appropriate warnings. With the advent of computer‐based simulation techniques, computer‐based data processing capabilities, and computer‐based communication facilities, the impact of hydroinformatics on flood forecasting in support of flood warning is manifest. In this article, an overview is given of flood forecasting systems for providing warnings in hydrological catchments. This overview is given from the perspective of the position of flood forecasting within the process of detection, forecasting, warning, and response. A categorization of flood forecasting systems is introduced, and the elements of a flood forecasting system are discussed.
Digital Elevation Model Analysis and Geographic Information Systems
Authors: Moglen Glenn E , Maidment David R 
Published: April 2006

Abstract
This article presents the technology of Geographic Information Systems (GIS) applied to a particular form of representation of topography, the digital elevation model (DEM). It first defines what a DEM is and introduces the basic properties of all DEMs, as well as several common sources of DEM data. Then the basic concepts of GIS technology are presented, defining what a GIS is, what fundamental data types it can store, and what kind of manipulations it can perform. Some of the most common GIS software packages are discussed. The remainder of the article focuses on the use of GIS technology for the interpretation of DEM in a hydrologic context. The principles of flow direction, flow accumulation, watershed delineation, flow lengths, slopes, and travel times as derived from DEM data within a GIS are presented. A brief case study is presented illustrating a number of the concepts presented in this article.
Weather Patterns and Weather Types
Authors: McKendry Ian G 
Published: April 2006

AbstractIn popular usage, the terms “weather pattern” and “weather type” are used variously and often imprecisely to describe states of the atmosphere. An understanding of weather processes and patterns has important applications in such diverse areas as air‐quality management, hydrology, water management, human health, forestry, agriculture, energy demand, transportation safety, the insurance industry, economics, and tourism. These terms are formally defined and the various classification techniques that form the basis of synoptic climatology are described. In summarizing the various methods used to identify weather patterns and types, it is abundantly clear that underlying such approaches are significant assumptions about the state of the atmosphere together with varying degrees of subjectivity inherent in the techniques themselves. It is important that these constraints are adequately acknowledged in all applications of the techniques outlined. Finally, the impacts of computing advances, new techniques, and enhanced datasets on synoptic climatology are described.
Models of Clouds, Precipitation and Storms
Authors: Flossmann Andrea I 
Published: April 2006

Abstract
Clouds play an important role for life on earth. Apart from influencing, for example, the radiative balance of the atmosphere and the lifetime of atmospheric trace constituents, they are the essential element in the hydrological cycle. Clouds transport the evaporated water of the oceans to the continents where the precipitation releases the water load. This release of water can be more or less vigorous depending on the energy stored in the cloud in the form of condensed hydrometeors (liquid or solid). This energy depends on the amount of available moisture and the way the vertical lifting necessary for cloud formation proceeds. We distinguish here mainly two different forms with varying extensions on the horizontal scale: the gentle uplift associated to the large‐scale lifting, for example at a frontal zone, and the vigorous small‐scale ascent associated with convection, knowing that also mixed forms of the lifting occur.
This article provides an introduction to the complex subject of modeling clouds, the production of precipitation, and the development of cloud and storm systems. The elements intervening in cloud modeling are exposed, starting from a description of the physical phenomena. On the basis of the occurring scale problem, a number of approaches for simplification are presented. These simplifications concern the dynamics as well as the microphysics. Bulk and bin modeling approaches are explained, as well as cumulus parameterizations. Some numerical problems are discussed. This approach gives an insight into current state‐of‐the‐art cloud modeling and the necessary balance between the degree of parameterization, the number of physical and chemical processes relevant to a particular problem, and the available computing resources.
Rainfall Trend Analysis: Return Period
Authors: Clarke Robin T 
Published: April 2006

Abstract
This article describes the concept of return period, with particular reference to the analysis of rainfall records. Methods are described for calculating return levels, corresponding to different return probabilities, when rainfall is accumulated over different time intervals. In the case of intense, short‐duration rainfalls, threshold models are illustrated. The article points out that the concept of return period is most easily interpreted where stationarity in the rainfall regime can be assumed, so that it is important to establish whether rainfall records show evidence of trends over time. Procedures are discussed for testing whether time trends exist in annual and monthly rainfall, in the occurrence and magnitude of daily rainfalls, and in annual maximum rainfall intensities over different durations. Where a trend in rainfall regime is apparent, an alternative to the concept of return period is suggested, on the basis of the probability of occurrence of an extreme event of specified magnitude, during a period extending into the future during which the observed trend can be assumed to continue.
Fog as a Hydrologic Input
Authors: Sampurno Bruijnzeel LA , Eugster Werner , Burkard Reto 
Published: April 2006

AbstractThis article reviews the hydrologic importance of fog in its various forms. Meteorologically, fog is defined as a ground‐touching cloud with a visibility in the horizontal of less than 1000 m. The most widely occurring fog types include radiation fog, sea fog and steam fog, and advection fog, but often fog is also referred to by its location of occurrence (coastal, valley, or mountain fog). The physical processes underlying the various types of fog are described briefly. The use, advantages, and limitations of the most common types of fog collectors, fog detectors, and fog droplet spectrometers are dealt with before embarking on a discussion of techniques for the measurement and modeling of fog deposition on forest vegetation. Results of fog deposition measurements made at selected locations (representing coastal vs. inland, lowland vs. montane, and temperate vs. tropical conditions) are compared. The data confirm the importance of fog interception at many coastal and montane sites across the tropical to mediterranean and warm‐temperate climatic spectrum. Under more continental conditions, contributions by fog are usually more modest except on windy mountain ridges and summits. Finally, the paper indicates the chief gaps in knowledge regarding the measurement and importance of fog as a hydrologic input.
Evaporation Modeling: Potential
Authors: Allen Richard G 
Published: April 2006

Abstract

Potential evaporation (
E
p
) has had a relatively broad range of definition over the past century. It is defined here as the quantity of water evaporated per unit area per unit time from an idealized extensive free‐water surface under existing atmospheric conditions. Three primary, common means to estimate
E
p
have been used during the past century. These are (i) pan evaporation measurement, (ii) an estimate of potential evapotranspiration based on weather data, and (iii) a reference evapotranspiration. Of these three, reference evapotranspiration (
ET
ref
) has the more practical application. “Potential evapotranspiration” (
ET
p
) had widespread usage from the 1940s through the 1970s, when the term was used to represent a maximum evaporative index from which to derive estimates of actual
ET
from vegetation. However, there are several major, contrasting definitions for
ET
p
and several challenges associated with its usage. One of the primary definitions used for
ET
p
is the rate of evaporation and transpiration from a saturated (free‐water) vegetated surface so that the evaporation process occurs at the potential level. Challenges in sustaining a saturated surface and in measuring weather data that are coincident with such a surface make this definition for
ET
p
theoretically attractive, but practically difficult. Standardized parameterizations of the Penman–Monteith equation are described for calculating
ET
for grass and alfalfa references. The reference evapotranspiration, despite some shortcomings, can be a consistent and reproducible index for a weather‐based potential evaporation.