Lecture 11: Metalloproteins - I

Transcription

1 Lecture 11: Metalloproteins - I 1. Introduction A large number of biochemical reactions are known to be catalyzed by proteins. The reason behind their functions as catalysts is attributed to the side chains of amino acid up to some extent and majorly to their ability to incorporate various cofactors such as metal ion, clusters, and organic molecules into their active site. About half of available proteins require metal ions at their active site to function. Proteins possessing one or more metal ions execute ample number of functions and are known as metalloproteins or metalloenzymes. The functionality of enzymes varies with the metal centre at their active site. For instance oxidation and reduction process generally involve, Mn, Cu and Mo; Co plays important role in radical-based rearrangement and methyl-group transfer reaction; Zn,, Mg, Mn and Ni are important for hydrolysis process and DNA processing involves Zn. Apart from this metalloenzymes are also involved in various cell function such as storage and transport of proteins, enzymes and signal transduction proteins. 2. Metal-coordination sites The usual coordination around the metal center in metalloproteins involves nitrogen, oxygen or sulfur atoms belonging to various amino acid residues of the protein. The functional groups involved in coordination, often comes from the side chain of amino acid residues. Among those imidazole substituent in histidine residues, thiolate substituents in cysteinyl residues, and carboxylate groups provided by aspartate are the most important one. Apart from these the peptide backbone participate in coordination, generally via deprotonated amides and the carbonyl oxygen centres of amide bond. In addition to this, a large number of organic cofactors acts as ligands. The most popular are the tetradentate N4 macrocyclic ligands incorporated into the heme protein. Inorganic ligands such as sulfide and oxide are also common.

2 Functional classification of metalloprotein Function Protein Metal/Metal Complexes PDB Electron Transfer Cytochrome b5 Adrenodoxin Plastocyanin heme b 22 Cu 1CYO 1AYF 1AG6 Light harvesting Light harvesting complex LH-II BChl-a 1KZU Catalysis torage (uptake,binding and release) Nitrile hydratase DMO reductase Nitrogenase Mo protein Manganese superixide dismutase Nitrophorin Hemocyanin Metallothioneins Lactoferrin Bacterioferritin Moco Moco Mn Heme(coordinates NO) 2Cu 2+ (coordinates O2) Cd 2+, Hg 2+, Pb 2+, Tl + (in form of hydrated ferric phosphate) 2AHJ 1DMR 3MIN 1VEW 4NP1 1OXY 4MT2 1B1X 1BFR Translocation Copper transporting ATPase Cu + 2AWO Various Lignin peroxidase Zinc finger Endonuclease III Ca 2+ Zn B82 1AAY 2ABK 3. torage and transport metalloprotein 3.1 Oxygen carriers Hemoglobin and myoglobin The two of the earliest structurally characterized proteins hemoglobin (Hb) and myoglobin (Mb) contain iron protoporphyrin IX (heme) as a prosthetic centre. Both the proteins bind reversibly with O2 however their biological role is different. Hb transport oxygen in blood plasma whereas, Mb accumulates O2 in cellular tissue. Hb contains four sub-units in which the (II) ion is coordinated by the planar, macrocyclic ligand protoporphyrin IX and the imidazole nitrogen atom of a histidine residue. The sixth coordination site encloses a water molecule or a dioxygen moiety. On the other side myoglobin has only one such unit and the active site is located in a hydrophobic pocket. The four subunits of hemoglobin show cooperativity effect which allows it to transfer oxygen to myoglobin.

3 Hemoglobin (PDB ID:1GZX) Myoglobin The diamagnetic nature of both the protein is attributed to low-spin state of (II). Both Hb and Mb bind O2 in the reduced state. The iron atom is located in the plane of the porphyrin ring in oxyhemoglobin, whereas it lies above the plane of the ring in deoxyhemoglobin Hemerythrin and Hemocyanin Non heme proteins like hemerythrin and hemocyanin, found only in invertebrates, are another class of oxygen carrier protein. Hemerythrin is an iron containing protein in which O2 binds at binuclear iron center. The coordination environment around iron atoms involves carboxylate side Hemerythrin Hemocyanin chains of glutamate and aspartate and five histidine residues. Reduction of binuclear iron center occurs upon oxygen uptake by hemerythrin results in production of bound peroxide (OOH-). Hemocyanin is most efficient in oxygen transport after hemoglobin. It contains binuclear copper

4 (I) ion. Upon oxygenation O2 reduced to peroxide (O2 2- ) consequently the two copper (I) atoms at the active site are oxidized to copper(ii). 3.2 Electron transfer Cytochromes Cytochromes are membrane bound heme containing proteins and are mainly responsible for ATP generation via electron transport. Cytochromes use redox behavior of 2+ / 3+ which act as electron-transfer vectors. Cytochromes are thus, proficient in performing oxidation and reduction reactions. Moreover since the cytochromes are apprehended within membranes, the redox reactions are Cytochrome c carried out in the proper sequence for maximum efficiency. Most of the cytochromes contained iron atom in a heme group. They differ in their side chains. For example cytochrome a has a heme a prosthetic group and cytochrome b has a heme b prosthetic group. everal cytochromes are involved in the mitochondrial electron transport chain due to difference in 2+ / 3+ redox potentials arises from different prosthetic group. Insertion of oxygen atom into C H bond an oxidation reaction is catalyse by cytochrome P Rubredoxin It is an electron-carrier protein found in sulfur-metabolizing bacteria and archaea. It governs one electron transfer processes. The active site of rubrdoxin consists of iron ion which is coordinated by the sulphur atoms of four cysteine residues in a tetrahedron arrangement. The oxidation state of central iron atom switches amidst the +2 and +3 oxidation states. The metal ion remains in high spin state in both the oxidation state, which minimizes any structural changes.

5 Rubredoxin active site Plastocyanin Plastocyanin belongs to blue copper proteins family which participates in electron transfer reactions. The preferred ligand geometry around copper atom is described as a distorted trigonal pyramidal. Two nitrogen atoms of different histidines and a sulfur atom from cysteine forms the base of the pyramidal whereas methionine forms the apex by introducing an axial sulfur. The difference in bond length of two distinguished Cu- bond causes rise in the redox potential of the protein. An absorption band appears at 597 nm due to the Cu- bond, accounts for the blue color. In the reduced form of plastocyanin, His-87 will become protonated with a pka of 4.4. Protonation prevents it acting as a ligand and the copper site geometry becomes trigonal planar. Plastocyanin Plastocyanin (PDB ID: 3BQV)