Sandbox Reserved 1096: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 5: | Line 5: | ||
==General Description== | ==General Description== | ||
<Structure load='4N20' size='450' frame='true' align='right' caption='Insert caption here' scene='82/829349/Main_domains_calcium/1'/> | <Structure load='4N20' size='450' frame='true' align='right' caption='Insert caption here' scene='82/829349/Main_domains_calcium/1'/> | ||
'''''Protein Arginine Deiminase type 2 ''''' also known as '''''PAD2''''', is a calcium-dependent [https://en.wikipedia.org/wiki/Enzyme enzyme] that catalyzes in humans the conversion of [https://en.wikipedia.org/wiki/Arginine Arginine] residues into [https://en.wikipedia.org/wiki/Citrulline Citrulline] in a [https://en.wikipedia.org/wiki/Post-translational_modification post-translational modification] referred to as [https://en.wikipedia.org/wiki/Citrullination Citrullination]. The structure of '''''PAD2 Apoenzyme''''' described here was elucidated at a calcium concentration of 0mM (Ca2+) with a resolution of 1.657 Å by [https://en.wikipedia.org/wiki/X-ray_crystallography x-ray diffraction cristallography]<ref name="PDB">[https://www.rcsb.org/structure/4N20</ref> . The biological assembly of PAD2 consists of a head-to-tail dimer with immunoglobin-like domains and a nucleophilic [https://en.wikipedia.org/wiki/Cysteine cysteine] residue responsible of catalytic activity in the active site <ref name="ART1">DOI:10.1021/cb500933j</ref>. In humans, five genes clustered in a single locus code for Arginine deiminases: ''PADI1,PADI2,PADI3,PADI4,PADI6''<ref name="ARTFr">DOI:10.1051/medsci/201127149</ref>. Expression of different [https://en.wikipedia.org/wiki/Protein_isoform isoforms] of PAD seem to depend strongly on cell types and tissues even though PAD2 may be an ubiquist protein <ref name="ARTFr" />. Peptidyl Arginine Deiminase type 2 appears to have an essential role in the development of [https://en.wikipedia.org/wiki/Breast_cancer Breast Cancer] <ref name="ART1" />, [https://en.wikipedia.org/wiki/Multiple_sclerosis Multiple Sclerosis(MS)]<ref name="ARTMS">DOI:10.1051/medsci/201127149</ref> and other degenerative disorders such as [https://en.wikipedia.org/wiki/Rheumatoid_arthritis Rheumatoid Arthritis] <ref name="ARTFr" /> thus making it a potential target for inhibitor design treatments. Related structures for PAD2 include: [[4n2b]] and [[4n2c]]. | '''''Protein Arginine Deiminase type 2 ''''' also known as '''''PAD2''''', is a calcium-dependent [https://en.wikipedia.org/wiki/Enzyme enzyme] that catalyzes in humans the conversion of [https://en.wikipedia.org/wiki/Arginine Arginine] residues into [https://en.wikipedia.org/wiki/Citrulline Citrulline] in a [https://en.wikipedia.org/wiki/Post-translational_modification post-translational modification] referred to as [https://en.wikipedia.org/wiki/Citrullination Citrullination]. The structure of '''''PAD2 Apoenzyme''''' described here was elucidated at a calcium concentration of 0mM (Ca2+) with a resolution of 1.657 Å by [https://en.wikipedia.org/wiki/X-ray_crystallography x-ray diffraction cristallography]<ref name="PDB">[https://www.rcsb.org/structure/4N20</ref> . The biological assembly of PAD2 consists of a head-to-tail dimer with <scene name='82/829349/Igg_domains/1'>immunoglobin-like domains</scene> and a nucleophilic [https://en.wikipedia.org/wiki/Cysteine cysteine] residue responsible of catalytic activity in the active site <ref name="ART1">DOI:10.1021/cb500933j</ref>. In humans, five genes clustered in a single locus code for Arginine deiminases: ''PADI1,PADI2,PADI3,PADI4,PADI6''<ref name="ARTFr">DOI:10.1051/medsci/201127149</ref>. Expression of different [https://en.wikipedia.org/wiki/Protein_isoform isoforms] of PAD seem to depend strongly on cell types and tissues even though PAD2 may be an ubiquist protein <ref name="ARTFr" />. Peptidyl Arginine Deiminase type 2 appears to have an essential role in the development of [https://en.wikipedia.org/wiki/Breast_cancer Breast Cancer] <ref name="ART1" />, [https://en.wikipedia.org/wiki/Multiple_sclerosis Multiple Sclerosis(MS)]<ref name="ARTMS">DOI:10.1051/medsci/201127149</ref> and other degenerative disorders such as [https://en.wikipedia.org/wiki/Rheumatoid_arthritis Rheumatoid Arthritis] <ref name="ARTFr" /> thus making it a potential target for inhibitor design treatments. Related structures for PAD2 include: [[4n2b]] and [[4n2c]]. | ||
==Structural Features== | ==Structural Features== | ||
==='''Primary, secondary and tertiary structure'''=== | ==='''Primary, secondary and tertiary structure'''=== | ||
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 active site (C647, 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 active site<ref name="ART1" />. Other key residues include D125, D127, E131 and E354 which may play an important role in Calcium binding for sites Ca1 and Ca2 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 active site. Both immunoglobin-like domains 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. | 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 active site (C647, 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 active site<ref name="ART1" />. Other key residues include D125, D127, E131 and E354 which may play an important role in Calcium binding for sites Ca1 and Ca2 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 active site. 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. | ||
==='''Calcium binding sites and active site'''=== | ==='''Calcium binding sites and active site'''=== | ||