### A. Overview

Extracellular purines (adenosine, ADP, and ATP) and pyrimidines (UDP and UTP) are important signaling molecules that mediate diverse biological effects via cell-surface receptors termed purine receptors. In this review particular emphasis is placed on the discrepancy between the

/pdf/receptors-for-purines-and-pyrimidines-56f78tnpew.pdf

Receptors for Purines and Pyrimidines

For present purposes, a protein-bound metal site consists of one or more metal ions and all protein side chain and exogenous bridging and terminal ligands that define the first coordination sphere of each metal ion. Such sites can be classified into five basic types with the indicated functions: (1) structural -- configuration (in part) of protein tertiary and/or quaternary structure; (2) storage -- uptake, binding, and release of metals in soluble form: (3) electron transfer -- uptake, release, and storage of electrons; (4) dioxygen binding -- metal-O{sub 2} coordination and decoordination; and (5) catalytic -- substrate binding, activation, and turnover. The authors present here a classification and structure/function analysis of native metal sites based on these functions, where 5 is an extensive class subdivided by the type of reaction catalyzed. Within this purview, coverage of the various site types is extensive, but not exhaustive. The purpose of this exposition is to present examples of all types of sites and to relate, insofar as is currently feasible, the structure and function of selected types. The authors largely confine their considerations to the sites themselves, with due recognition that these site features are coupled to protein structure at all levels. In themore » next section, the coordination chemistry of metalloprotein sites and the unique properties of a protein as a ligand are briefly summarized. Structure/function relationships are systematically explored and tabulations of structurally defined sites presented. Finally, future directions in bioinorganic research in the context of metal site chemistry are considered. 620 refs.« less

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Structural and Functional Aspects of Metal Sites in Biology

Protein phosphorylation and regulation of adaptive responses in bacteria.

ion step follows the decarboxylation, which is consistent with the deuterium isotopic effects observed for thymine 7-hydroxylase which indicate that an irreversible step (or steps) occurs prior to the C-H bond breaking.395 It has also been shown for prolyl 4-hydroxylase that a substrate-derived radical is generated in the reaction, which is consistent with a rebound mechanism.437 It is important to point out that no oxygen intermediate (i.e., bridged superoxo or oxo-ferryl) has been observed for any R-KGdependent enzyme. This warrants future theoretical and experimental study. A detailed molecular mechanism has been proposed for IPNS based on spectroscopic and crystallographic studies.422 Resting IPNS/FeII is also 6C and thus relatively stable toward dioxygen. Substrate ACV binds directly to FeII IPNS through its thiolate group, providing an open coordination position at the FeII. O2 can then react to form an FeIII-superoxo intermediate. This intermediate is suggested422 to perform the first hydrogen-atom abstraction step and close the â-lactam ring, resulting in the formation of the first water molecule and generating an FeIVdO-II intermediate, which completes the second ringclosure process by hydrogen-atom abstraction forming a thiazolidine ring. Previously proposed mechanisms of ACCO involved direct binding of cosubstrate ascorbate to the iron before O2 as part of the oxygen activation process.438,439 The EPR and ESEEM studies of the NO complex of ACCO suggested a quite different molecular mechanism for ACCO.435 An FeIII-superoxo intermediate is proposed. Whether it is preceded by a 6C f 5C process with substrate binding is presently under study.440 This intermediate is thought to initiate a radical process by single hydrogen-atom abstraction or electron-coupled proton transfer (PT)ion or electron-coupled proton transfer (PT) from the bound amino group. The resulting substrate radical may undergo spontaneous conversion into products. The role of cosubstrate ascorbate is proposed to reduce the toxic peroxo byproduct to water. Alternatively, the two-electron reduction of FeIIIsuperoxo by the cosubstrate ascorbate could result in an FeIVdO-II intermediate which initiates the radical reaction.435 4. Rieske-Type Dioxygenases Biochemical Characterization. The Rieske ironsulfur center is a two iron-two sulfur cluster ([2Fe2S]) which has a 2His (on one iron), 2Cys (on the other iron) coordination environment, instead of the 4Cys present in plant ferredoxins. It plays a key role in the electron transport pathway in membranebound cytochrome complexes as well as in some dioxygenases.441 The latter are mainly comprised of two protein components: a reductase containing flavin and a ferredoxin [2Fe-2S], and a terminal oxygenase containing a Rieske [2Fe-2S] cluster and a non-heme iron active site.442 Except for the recently reported alkene monooxygenase that has a binuclear iron site in its terminal oxygenase,10 most of the Rieske-type oxygenases have a mononuclear iron site, which is believed to be the site of dioxygen activation and substrate oxygenation.442,443 The majority of the Rieske-type mononuclear non-heme oxygenases form a family of enzymes which are aromatic-ring-hydroxylating dioxygenases. These catalyze the regioand stereospecific cis-dihydroxylation of an aromatic ring using dioxygen and NAD(P)H (Table 1). Examples include benzene dioxygenase (BDO, EC 1.14.12.3),444 phthalate dioxygenase (PDO, EC 1.14.12.7),445 toluene dioxygenase (EC 1.14.12.11),446 and naphthalene 1,2-dioxygenase (NDO, EC 1.14.12.12),447 which initiate the aerobic degradation of aromatic compounds in the soil bacteria and are targets for bioengineering in bioremediation. This step is the first step in the pathway that ultimately leads to ring cleavage by the intraand extradiol dioxygenases (sections II.B.2 and II.C.1).443 Besides these bacterial dioxygenases, other Rieske-type mononuclear non-heme oxygenases include anthranilate 1,2-dioxygenase (EC 1.14.12.1),448 which deaminates and decarboxylates the substrate to produce catechol; chlorophenylacetate 3,4-dioxygenase (EC 1.14.2.13),449 which converts substrate to catechol with chloride elimination; and 4-methoxybenzoate O-demethylase (putidamonooxin),450 which catalyzes the conversion of 4-methoxybenzoic acid to 4-hydroxybenzoic acid and formaldehyde. The reductase component is usually a monomer (MW ) 12-15 kDa) and utilizes flavin to mediate ET from the two-electron donor NAD(P)H to the oneelectron acceptor [2Fe-2S] cluster and is specific to each terminal oxygenase; other electron donors do not support efficient oxygenation.442 The crystal structure of phthalate dioxygenase reductase is available.451 The terminal oxygenases are large protein aggregates (MW ) 150-200 kDa) containing either multiples of R subunits (BDO R2, PDO R4) or an equimolar combination of R and â subunits (toluene dioxygenase R2â2, NDO R3â3). The R subunits contain a Rieske [2Fe-2S] cluster and a catalytic non-heme FeII center. â subunits do not seem to be involved in the catalytic function (vide infra). Kinetics. Steady-state kinetic studies coupled with various rapid reaction studies of the partial reactions of PDO allowed Ballou et al. to propose a kinetic scheme (Scheme 15).443 On the basis of steady state 278 Chemical Reviews, 2000, Vol. 100, No. 1 Solomon et al.

Geometric and Electronic Structure/Function Correlations in Non-Heme Iron Enzymes

Calcineurin is a eukaryotic Ca2+- and calmodulin-dependent serine/threonine protein phosphatase. It is a heterodimeric protein consisting of a catalytic subunit calcineurin A, which contains an act...

https://www.physiology.org/doi/pdf/10.1152/physrev.2000.80.4.1483

Calcineurin : form and function

Anorganisch-Chemisches Institut der Universitat Munster, Wilhelm-Klemm-Strasse 8, 48 149 Munster, Germany, Fachgebiet Anorganische ChemieFestkorperchemie der Universitat Duisburg, Lotharstrasse 1, 47057 Duisburg, Germany, Institut f i r Biochemie der Universitat Munster, Wilhelm-Klemm-Strasse 2, 48 149 Munster, Germany, and European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany

XAS Investigations on the Iron-Zinc Center of Purple Acid Phosphatase from Red Kidney Beans

Dinucleosid-phosphate aus Hefe-ribonucleinsäure durch Hydrolyse in Gegenwart von Wismuthydroxyd

Einfluss der Nucleotidbasen auf die nicht-enzymatische Spaltung der Ribonucleinsäure-diester-Bindungen

Crystallization and preliminary crystallographic data of purple acid phosphatase from red kidney bean.

Proton magnetic resonance (PMR) spectra of 45 nucleoside and nucleotide derivatives of uracil, thymine, cytosine, 5-methylcytosine, and other substituted pyrimidines in water or dimethyl sulfoxide solutions have been analysed in order to correlate structure variations with molecular conformations and to gain insight into the nature of intramolecular forces which are responsible for the ‘rigidity’ of the molecules. Irrespective of the structure of pyrimidine base and the absolute chemical shift values (δ) the C(6)-H and, to a lesser degree, the C(5)-H and C(5)-CH3 resonances are shifted downfield by very similar amounts (Δδ) in the regular nucleosides or in the presence of charged or polar C-4′ substituents. In detail, the following conformation-determining effects are seen.



1. Ribose vs 2-deoxyribose substitution of a pyrimidine makes little difference for the chemical environment of base hydrogens but an intact pentofuranose ring (4′-O) and the exocyclic 5′-OH group are essential for a nucleoside to assume a specific conformation.



2. Profound shielding or deshielding of H-6 by exocyclic nitrate, halogen, hydroxyl, phosphate, and carboxylate substituents indicates preference for the anti and gauche, gauche conformation ranges in all compounds except in the case of C-6 substitution.



3. Halogen atoms and the hydroxyl group (Δδ∼ 0.30–0.40 ppm) interact with pyrimidine bases by induced polarisation of the C(5)=C(6) double bond, phosphate anions (Δδ∼ 0.50 ppm) interact by the electrostatic attraction mechanism previously described, and in nucleoside 5′-carboxylates (Δδ > 0.90 ppm) a hydrogen bond between −COO− and H-6 is formed.



4. The deshielding effects caused by a 5′-OH group and monoanionic 5′-phosphate are similar (Δδ∼ 0.35–0.45 ppm), supporting the view that intramolecular rigidity of nucleosides and the nucleotide unit is not fundamentally different.



This systematic survey, together with our previous studies of adenosine derivatives, provides a rationale for why the majority of both pyrimidine and purine nucleosides and nucleotides in solution exhibit closely comparable conformations, which in turn explain the group specificity of certain key enzymes in nucleic acid metabolism.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1977.tb11686.x

Herbert Witzel

Papers

XAS Investigations on the Iron-Zinc Center of Purple Acid Phosphatase from Red Kidney Beans

Dinucleosid-phosphate aus Hefe-ribonucleinsäure durch Hydrolyse in Gegenwart von Wismuthydroxyd

Einfluss der Nucleotidbasen auf die nicht-enzymatische Spaltung der Ribonucleinsäure-diester-Bindungen

Crystallization and preliminary crystallographic data of purple acid phosphatase from red kidney bean.

Pyrimidine Nucleosides in Solution