Sandbox Reserved 1096: Difference between revisions

In terms of primary structure, the '''''apoenzyme''''' described under PDB's [https://www.rcsb.org/structure/4N20 4N20] contains 4 key catalytic residues that are essential for citrullination in the <scene name='82/829349/Active_site/1'>active site</scene> (<scene name='82/829349/C647/1'>C647</scene>, D351, H471 and D473). The cysteine residue is involved in nucleophilic attacks that promote deimination of Arginine residues whereas the other residues are mainly responsible for stabilization of substrates entering the <scene name='82/829349/Active_site/1'>active site</scene><ref name="ART1" />. Other key residues include D125, D127, E131 and E354 which may play an important role in Calcium binding for sites <scene name='82/829349/Ca1/1'>Ca1</scene> and <scene name='82/829349/Ca6/1'>Ca6</scene> given that side-chains are around 5Å away from Calcium cations. Considering both Aspartate and Glutamate are negatively charged at pH 7, electrostatic interactions may exist between these residues and Ca2+ in binding sites. In the other hand, the structure of '''''apoPAD2''''' shows some common secondary motifs such as superimposed anti-parallel beta sheets that generate beta sandiwiches. Closer to the C-terminal, both alpha and beta secondary structures may be observed with 17 alpha helixes and multiple parallel and anti-parallel beta sheets that make up an alpha/beta propeller<ref name="ART1" />. Tertiary structure of '''''apoPAD2''''' monomer is well described by [https://pubs.acs.org/doi/10.1021/cb500933j Slade et al.] as being composed of three distinct domains: 2 immunoglobin-like domains (IgG1 and IgG2) at positions (1-115)(116-295) respectively and a C-terminal catalytic domain at (296-665) that contains the <scene name='82/829349/Active_site/1'>active site</scene>. Both <scene name='82/829349/Igg_domains/1'>immunoglobin-like domains</scene> comprise typical beta-sandwiches and the catalytic domain generates an alpha/beta propeller. Finally, with respect to the quaternary structure, '''''PAD2 Apoenzyme''''' cristallises as a stable dimer of identical subunits (monomers). The biological assembly of the enzyme was thus observed to be an association of two monomers whose structural highlights were described above.         

PAD2 is a calcium-dependent enzyme which catalyzes the deimination of [https://en.wikipedia.org/wiki/Arginine Arginine] residues. This reaction occurs only if calcium ions bind to specific sites of PAD2 but they do not directly participate in [https://en.wikipedia.org/wiki/Catalysis catalysis] : they act as [https://en.wikipedia.org/wiki/Cofactor_(biochemistry) cofactors]. Once Calcium binding is accomplished, a '''''catalytic cysteine residue in position 647''''' in the peptide chain changes its position to carry out a [https://en.wikipedia.org/wiki/Nucleophilic_substitution nucleophilic attack] on [https://en.wikipedia.org/wiki/Guanidine  guanidinium] groups of arginine residues. In terms of specific catalysis at the active site of PAD2, four residues are essential for the progress of citrullination: <scene name='82/829349/Active_site/1'>D351, H471, D473</scene> and <scene name='82/829349/C647/1'>C647</scene><ref name="ART1" /><ref name="ARTC">McCoy, R.S., Braun-Sand, S.B. Semimicroscopic investigation of active site pK a values in peptidylarginine deiminase 4. Theor Chem Acc 131, 1293 (2012) [https://doi.org/10.1007/s00214-012-1293-9 DOI:10.1007/s00214-012-1293-9]</ref>. [https://en.wikipedia.org/wiki/Histidine Histidine] 471 and [https://en.wikipedia.org/wiki/Cysteine Cysteine] 647 are directly involved in deimination catalysis while [https://en.wikipedia.org/wiki/Aspartic_acid Aspartates] 351 and 473 facilitate the reaction by interacting with Arginine residues ([https://en.wikipedia.org/wiki/Substrate_(chemistry) substrates]) holding them in place inside the active site<ref name="ARTC" />. A mechanism of reaction has been proposed in which the nucleophilic attack of [https://en.wikipedia.org/wiki/Thiol thiolate] in C647 generates the cleavage of a carbon-nitrogen bond to form [https://en.wikipedia.org/wiki/Ammonia Ammonia]. A water molecule will then replace ammonia and, after hydrolysis of thiouronium intermediate, citrulline product is formed and the enzyme's active site is regenerated<ref name="ARTC" />. Arginine residue substrates can bind to PAD2 because calcium binding engenders a move out of the active site for an arginine in position 347 and a move in for a [https://en.wikipedia.org/wiki/Tryptophan tryptophan] in position 348 in order to form a pocket for the substrate<ref name="ART1" />.