bluuebunny/crossref_metadata_2025_split huggingface dataset:
TroponinC
Authors: Gagné Stéphane M 
Published: December 2011

AbstractRegulation of contraction in skeletal and cardiac muscle occurs through calcium binding to the protein troponin C (TnC). The N‐terminal domain of TnC (NTnC) carries out the regulatory role through the binding of calcium ions – two calcium ions in skeletal muscle and one in cardiac muscle.Thirty‐nine sequences of TnC have been sequenced so far. Of the 39 sequences of TnC, 5 have had their three‐dimensional structures determined in various forms by NMR and X‐ray. Available structures include 26 uncomplexed structures in various calcium states, and 13 structures in which cardiac and skeletal TnC is complexed with fragments of troponin I and/or troponin T.
Parvalbumin
Authors: Nakayama Susumu , Kawasaki Hiroshi , Kretsinger Robert H 
Published: December 2011

Abstract

Parvalbumin was the first EF‐hand protein to have been characterized and to have its crystal structure determined. This prototype consists of an α‐helix E (extended forefinger of a clenched right hand), loop around the Ca
2+
ion (clenched middle finger), and α‐helix F (extended thumb). Parvalbumin has provided a reference point for the analyses of 76 other subfamilies of proteins that contain 2 to 12 EF‐hands. Most, but not all, EF‐hands bind calcium. The Ca
2+
ion is almost always coordinated by seven oxygen atoms arranged in an approximate pentagonal bipyramid; usually one of the ligands is a carboxylate group that coordinates calcium with both its oxygen atoms. The affinities of EF‐hands for calcium range from p
K
d
(Ca
2+
) 6 to 8. The dissociation constant of parvalbumin for calcium (
K
d
∼ 10
−8
M) reflects one of the highest affinities of all the EF‐hand proteins. All, or most, of the EF‐hand proteins bind calcium ∼10
4.0
more strongly than they bind the six‐coordinate magnesium. Most of this difference in affinity derives from the ∼10
3.4
greater
on
rate for calcium, which in turn derives from its faster dehydration rate. Parvalbumin functions in fast, white, skeletal muscle to soak up messenger calcium following a stimulus, thereby facilitating rapid relaxation. Whether it has an analogous function in neurons, thymus, or other tissues remains to be demonstrated. Most EF‐hand proteins change conformation upon binding calcium, thereby transducing the information content of a pulse of cytosolic messenger Ca
2+
ions. Although the binding of calcium to the two EF‐hands of monomeric parvalbumin is not (or only very weakly) cooperative, as is the case for other EF‐hand proteins, the interaction of a pair of EF‐hands is essential for the stability of these proteins. The angle between the two helices (E and F) of a single EF‐hand as well as the contact between the pair of EF‐hands is usually more
open
following binding of calcium, thereby exposing hydrophobic side chains. However, a survey of the known structures of all known EF‐hands proteins does not reveal a bimodal
closed, open
set of conformations reflecting either binding of calcium and/or binding of targets for those EF‐hand proteins involved in information transduction.
PEFLINS: A Family of PentaEF‐Hand Proteins
Authors: Cygler Miroslaw 
Published: December 2011

AbstractPenta‐EF hand proteins, or PEFLINs, belong to the superfamily of regulatory Ca2+‐binding proteins with EF‐hand motifs. The calcium‐binding domain is ∼170 residues long and contains five EF‐hand motifs, of which only some retain the ability to bind calcium. Within individual molecules the (1st + 2nd) and (3rd + 4th) EF‐hands are associated in pairs while the 5th EF‐hand is unpaired. This domain is associated with an N‐terminal domain of varying length, usually 20 to 100 residues long and with a Gly/Pro‐rich region. Binding of Ca2+promotes association of these proteins with membranes, andin vitroleads to aggregation. On the basis of the 1st EF‐hand, these proteins are divided into two subfamilies. Calpain, grancalcin, and sorcin have a one‐residue deletion in the Ca2+‐binding loop between helices E and F and form a distinct variant of calcium binding. ALG‐2 and peflin have the canonical EF1 hand and bind calcium in a standard way. All penta‐EF hand proteins form homo‐ or heterodimers. The dimerization is promoted by pairing of the 5th EF‐hand of each molecule; thus in the dimer all EF‐hands are paired. Binding of Ca2+promotes only small, mostly local, conformational changes and it is plausible that binding of a concomitant partner molecule is required for larger rearrangements to occur.
3DStructures of the Calcium and Zinc BindingS100 Proteins
Authors: Fritz Günter , Heizmann Claus W 
Published: December 2011

AbstractS100 proteins are involved in many cellular processes such as cell growth and motility, cell cycle regulation, transcription, and differentiation. Twenty members have been discovered so far, and altogether, S100 proteins represent the largest subgroup within the EF‐hand Ca2+‐protein family. In resting cells, S100 proteins are localized in specific cellular compartments from which they relocate upon activation, hereby transducing the Ca2+/Zn2+signals by interacting with various target proteins. Some members are even secreted from cells exerting extracellular, cytokine‐like activities by interacting with the surface receptor RAGE.
Membrane BindingC2‐Like Domains
Authors: Verdaguer Nuria , Corbalán‐García Senena , Ochoa Wendy F , Gómez‐Fernández Juan Carmelo , Fita Ignacio 
Published: December 2011

AbstractC2‐domains are independently folded modules, of about 130 residues, found in a large and diverse set of eukaryotic proteins. Many of the best‐characterized C2‐domains are found in proteins involved in membrane trafficking and fusion, such as synaptotagmins or rabphilin, and in signal transduction, such as phospholipases A2 (cPLA2) and C (PLC) or the protein kinase C isoforms (PKCs). All C2‐domains share a common overall fold: a single compact Greek‐key motif organized as an eight‐stranded antiparallel β‐sandwich consisting of a pair of four‐stranded β‐sheets – the A and B sheets – with a long axis of about 50 Å. Connections between β‐strands emerge from the top and bottom of the domain according to the two distinct topologies of C2‐domains. In topology I (the S family), the first β‐strand occupies the same structural position as the eighth β‐strand of topology II (the P family), which shifts in a circular permutation the order of homologous strands in the primary structure. The structural information defines adjacent calcium binding sites within a broad acidic cleft that contains highly conserved acidic residues. These provide most of the oxygen atoms that coordinate with the calcium ions. The present work will focus on the wealth of functional and structural information, which is being obtained at an exponential pace, on the membrane‐binding C2‐domains that require calcium.
Dockerin Domains
Authors: Volkman Brian F , Lytle Betsy L , David Wu J H 
Published: December 2011

AbstractBacterial protein domains known as dockerins serve as anchoring or tethering modules for the assembly of large extracellular cellulase complexes called cellulosomes. Dockerins function through interactions with another class of protein‐interaction module, the cohesins, and both domain families are currently divided into two subclasses (type I and type II) originally based on binding specificity. Dockerin sequences contain a pair of 22‐residue motifs with homology to calcium‐binding loops of the EF‐hand family. When exposed to calcium, the dockerin adopts a novel fold distinct from EF‐hand proteins that binds its cognate cohesin with high affinity. Conversely, in the absence of calcium, the dockerin domain is unfolded and does not bind cohesin. Thus, dockerin domains serve as calcium‐regulated mediators of protein complex formation. Analysis of conserved sequence features in the context of the three‐dimensional dockerin structure may identify elements that confer class and species specificity of dockerin–cohesin binding reactions.
PhospholipaseA2
Authors: Betzel Christian , Singh Tej P , Georgieva Dessislava , Genov Nicolay 
Published: December 2011

AbstractPhospholipase A2s (phosphatidesn‐2 acylhydrolase, EC 3.1.1.4, PLA2) hydrolyze specifically thesn‐2 ester bond of phospholipids (PL). With some exceptions, they are Ca2+‐dependent enzymes. PLA2s are present in many organs and body fluids of vertebrates, invertebrates, and insects. They play an important role in the phospholipid digestion, remodeling, and metabolism, and are involved in human diseases such as acute pancreatitis, rheumatoid arthritis, respiratory distress, and acute chest syndrome. This review summarizes recent data on the biological function, amino acid sequence, classification, structure–function relationships, and 3D structures of PLA2s. Special attention is paid to the pharmacological activities of the snake venom enzymes. These hydrolases exert their activity through specific protein–protein interactions. Two types of structurally and functionally distinct receptors, N‐ and M‐type, were identified during the last decade and characterized. PLA2binding to its protein receptor can lead to cell damage, tissue necrosis, and other undesirable processes. The ‘interfacial activation’ of the enzymes and their participation in the interfacial catalysis are discussed. Protection of cell membranes from PLA2s is of medical importance.
Calsequestrin
Authors: Kang ChulHee 
Published: December 2011

AbstractThe contraction/relaxation of the muscle cell is controlled by the transient increase/decrease of Ca2+concentration. A large fraction of this Ca2+is stored in and released from the sarcoplasmic reticulum (SR) by the presence of high concentrations of an acidic protein, calsequestrin, in the lumen of the junctional terminal cisternae of SR. Calsequestrin binds and releases large quantities of Ca2+ion rapidly: about 40 to 50 ions per molecule with a binding constant of approximately 1 mM under physiological conditions. The cation binding by calsequestrin is nonspecific and the Ca2+binding sites incorporate the numerous acidic residues that comprise over one‐third of the total residues. The crystal structure of calsequestrin shows that it is made up of three domains, each with a thioredoxin fold. Ca2+ions are bound on the protein surface and between domains. Two distinct dimerization contacts in calsequestrin crystals suggested a mechanism for Ca2+regulation resulting from the occurrence of coupled Ca2+binding and protein polymerization. Ca2+‐induced formation of one contact was proposed to lead to dimerization followed by Ca2+‐induced formation of the second contact to bring about polymerization. Strong cooperative calcium binding accompanies the polymerization of calsequestrin into insoluble, extended, and often needle‐like structures. The polymerization of calsequestrin also provides a highly charged surface onto which calcium is adsorbed. A sparingly soluble ion such as Ca2+would tend to spread over the surface of the polymer, forming a readily exchangeable film. The propensity of Ca2+‐bound calsequestrin to form linear structures would make Ca2+dissociation and diffusion a more rapid event.
Myoglobin
Authors: Phillips George N 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsActivity TestStructural StudiesStructural Basis of Reversible Oxygen BindingSpectroscopic Studies on MyoglobinOther Structural Studies on MyoglobinFolding/Unfolding of MyoglobinRelated Articles
Cytochromef
Authors: Soriano Glenda M , Smith Janet L , Cramer William A 
Published: December 2011

AbstractCytochromef(f, folium, leaf), ac‐type cytochrome with a characteristic CysXXCysHis amino acid sequence for heme ligation, is the largest of the four major protein subunits of the membrane‐embedded cytochromeb6fcomplex of oxygenic photosynthesis. It contains 285–86 amino acids, consisting of a soluble 250‐residue domain on the p‐side (positive‐side) or lumen‐side of the membrane, a single trans‐membrane 20‐residue α‐helix, and an n‐ or stromal‐side segment consisting of 15 residues. These domains contain, respectively, the heme prosthetic group and intraprotein electron transfer pathway, the membrane anchor and a short segment that is important in the assembly of theb6fcomplex.The function of the cytochromefin oxygenic photosynthesis is to act as the terminal electron acceptor in the membrane‐embedded cytochromeb6fcomplex that provides the electron transport connection between the photosystem II and photosystem I reaction centers. Electron transfer through the complex is coupled to proton translocation and generation of a proton electrochemical potential that is utilized to drive the synthesis of ATP through the proton‐motive ATP synthase.These functions of the cytochromeb6fcomplex are analogous to those of the multisubunit cytochromebc1complex (ubiquinol:cytochromecoxidoreductase) of the mitochondrial respiratory chain and photosynthetic bacteria. Both complexes contain four redox centers with very similar redox and structural properties: a covalently boundc‐type heme in cytochromeforc1, the 2Fe–2S cluster of the Rieske ISP, and the two noncovalently bound hemes of cytochromeb. The structure properties have been defined in 3.0–3.1 Å structures of theb6fcomplex from a thermophilic cyanobacterium and a green alga. These structures also defined a fifth redox prosthetic group, a novel covalently bound heme, tentatively called hemex. With the exception of the extrinsic cytochromesfandc1that, except for the heme‐binding peptide sequence, are completely different, the redox‐active protein subunits of thebc1andb6fcomplexes are structurally similar. For theb6fcomplex, structures at the level of atomic resolution (<2 Å) have also been obtained for the p‐side or lumen‐side extrinsic domains of cytochromefand the Rieske high potential [2Fe–2S] protein, which together constitute approximately 40% of the total mass of the complex.
Cytochromecd1Nitrite Reductase
Authors: Allen James WA , Ferguson Stuart J , Fülöp Vilmos 
Published: December 2011

AbstractCytochromecd1catalyzes the one‐electron reduction of nitrite (NO2−) to nitric oxide and water. It is isolated from many bacteria, which respire by the process of denitrification.In vitro,cd1is also an oxidase and a hydroxylamine reductase. Each monomer of the dimeric enzyme contains onec‐type cytochrome center, which accepts electrons from donor proteins, and oned1heme, which is the active site and is unique to this class of enzymes. High‐resolution X‐ray structures have shown that in the oxidized forms, when isolated, the axial coordination of the hemes differs between the best‐studied cytochromescd1, the enzymes fromParacoccus pantotrophusandPseudomonas aeruginosa. Upon reduction, theP. pantotrophusenzyme undergoes a major and unprecedented conformational change and adopts the same heme coordinations as that of the reducedP. aeruginosacd1. The structural differences between the enzymes from these two sources are reflected in their biochemical, electron transfer, and spectroscopic properties.
CytochromecNitrite Reductase
Authors: Einsle Oliver 
Published: December 2011

AbstractNitrite (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

Abstract
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

AbstractRubredoxins 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

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.
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

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and Cluster TypeSpectroscopyNMRSolution Structure of NativeD. GigasFdIIFunctional AspectsStructural Cluster Interconversions: Synthesis of Heterometal ClustersAcknowledgementsRelated Articles
High Potential Iron Sulfur Proteins
Authors: Carter Charles W 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Production, Purification and Molecular CharacterizationMetal Content and CofactorsSpectroscopyActivity TestsX‐Ray Structures of NativeHiPIPModelFe4S4ComplexesFunctional AspectsElectron Transfer MechanismsAcknowledgmentsRelated Articles
Naphthalene 1,2‐Dioxygenase
Authors: Ramaswamy S 
Published: December 2011

AbstractNaphthalene 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

Abstract2,3‐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.