Sandbox Reserved 1104: Difference between revisions

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=====Covalent bond between Trp396 and His398=====

Since the discovery of bilirubin oxidase, two cristal structures of native enzyme have been published independently. The structure shown here and described by Cracknell ''et al.'' reveals that the imidazole ring of His398 —one of the T1Cu ligands — is abnormally close to the indole ring of Trp396, which raises the possibility that there is a <scene name='82/829357/Trp-his_covalent_bond/1'>His–Trp link</scene>. On the contrary in the structure described by Mizutani ''et al.'' (cf [[3abg]]) the indole ring of Trp396 turns away and does not form the covalent bond with the imidazole ring of His398 <ref name="stru">DOI: 10.1002/chem.201803798</ref>.

Since the discovery of bilirubin oxidase, two cristal structures of native enzyme have been published independently. The structure shown here and described by Cracknell ''et al.'' reveals that the imidazole ring of His398 —one of the T1Cu ligands — is abnormally close to the indole ring of <scene name='82/829357/Trp396/1'>Trp396</scene>, which raises the possibility that there is a <scene name='82/829357/Trp-his_covalent_bond/1'>His–Trp link</scene>. On the contrary in the structure described by Mizutani ''et al.'' (cf [[3abg]]) the indole ring of <scene name='82/829357/Trp396/1'>Trp396</scene> turns away and does not form the covalent bond with the imidazole ring of His398 <ref name="stru">DOI: 10.1002/chem.201803798</ref>.

Several studies proved that bilirubin oxidase has actually a post-translationally formed covalent bond between the imidazole ring of His398 coordinated to type I copper and the indole ring of Trp396 <ref name="stru"/><ref>DOI: 10.1016/j.bbrc.2019.10.159</ref><ref name="struct">DOI: 10.1038/s41598-019-50105-3</ref>. Indeed, the distance between Trp396 and His398 is 1.9 Å, which is shorter than the Van der Waals distance. Moreover, the torsion angle between the side chain rings of Trp396 and His398 is 65°, suggesting that the covalent link comprises a single bond <ref name="stru"/>.

Several studies proved that bilirubin oxidase has actually a post-translationally formed covalent bond between the imidazole ring of His398 coordinated to type I copper and the indole ring of <scene name='82/829357/Trp396/1'>Trp396</scene> <ref name="stru"/><ref>DOI: 10.1016/j.bbrc.2019.10.159</ref><ref name="struct">DOI: 10.1038/s41598-019-50105-3</ref>. Indeed, the distance between <scene name='82/829357/Trp396/1'>Trp396</scene> and His398 is 1.9 Å, which is shorter than the Van der Waals distance. Moreover, the torsion angle between the side chain rings of <scene name='82/829357/Trp396/1'>Trp396</scene> and His398 is 65°, suggesting that the covalent link comprises a single bond <ref name="stru"/>.

Among the multicopper oxidases, bilirubin oxidase is the only one which forms this <scene name='82/829357/Trp-his_covalent_bond/1'>His-Trp link</scene>. It is due to the particular molecular environment of the Trp396 residue, which is unique among the multicopper oxidases registered in the PDB. Indeed, the equivalent position is occupied by a glutamate side chain in multicopper oxidases from ''Thermus thermophilus'' ([[2xu9]]) and ''Campylobacter jejuni'' ([[3zx1]]), by aspartate in yeast Fet3p ([[1zpu]]), and by a main chain carbonyl oxygen atom in laccases from ''Antrodiella faginea'' ([[5ehf]]), ''Cerrena maxima'' ([[5h5u]]), ''Coriolus zonatus'' ([[2hzh]]), ''Lentinus sp.'' ([[3x1b]]), ''Lentinus tigrinus'' ([[2qt6]]), ''Steccherinum murashkinskyi'' ([[5mig]]), ''Trametes hirsuta'' ([[3fpx]]), and ''Trametes sp.'' AH28-2 ([[3kw7]]) <ref name="stru"/>.

Among the multicopper oxidases, bilirubin oxidase is the only one which forms this <scene name='82/829357/Trp-his_covalent_bond/1'>His-Trp link</scene>. It is due to the particular molecular environment of the <scene name='82/829357/Trp396/1'>Trp396</scene> residue, which is unique among the multicopper oxidases registered in the PDB. Indeed, the equivalent position is occupied by a glutamate side chain in multicopper oxidases from ''Thermus thermophilus'' ([[2xu9]]) and ''Campylobacter jejuni'' ([[3zx1]]), by aspartate in yeast Fet3p ([[1zpu]]), and by a main chain carbonyl oxygen atom in laccases from ''Antrodiella faginea'' ([[5ehf]]), ''Cerrena maxima'' ([[5h5u]]), ''Coriolus zonatus'' ([[2hzh]]), ''Lentinus sp.'' ([[3x1b]]), ''Lentinus tigrinus'' ([[2qt6]]), ''Steccherinum murashkinskyi'' ([[5mig]]), ''Trametes hirsuta'' ([[3fpx]]), and ''Trametes sp.'' AH28-2 ([[3kw7]]) <ref name="stru"/>.

The role of this covalent bond between the indole ring of Trp396 and the imidazole ring of His398 has been investigated using mutants of bilirubin oxidase (at the position 396). Their enzymatic activities have been compared with the one of wild type bilirubin oxidase. All the mutations have led to a significant decrease of the catalytic efficiency for bilirubin, compared to the wild type bilirubin oxidase. It proves that the <scene name='82/829357/Trp-his_covalent_bond/1'>Trp396-His398</scene> covalent bond has a major role in the enzymatic activity of bilirubin oxidase. However, it has no influence on the enzyme structure (except the replaced residue), since bilirubin can still bind to mutants not containing tryptophan at the position 396. Moreover, bilirubin is oxidized even in the absence of the Trp-His covalent bond, proving that its role in electron transfer is not crucial <ref name="struct"/>.

The role of this covalent bond between the indole ring of <scene name='82/829357/Trp396/1'>Trp396</scene> and the imidazole ring of His398 has been investigated using mutants of bilirubin oxidase (at the position 396). Their enzymatic activities have been compared with the one of wild type bilirubin oxidase. All the mutations have led to a significant decrease of the catalytic efficiency for bilirubin, compared to the wild type bilirubin oxidase. It proves that the <scene name='82/829357/Trp-his_covalent_bond/1'>Trp396-His398</scene> covalent bond has a major role in the enzymatic activity of bilirubin oxidase. However, it has no influence on the enzyme structure (except the replaced residue), since bilirubin can still bind to mutants not containing tryptophan at the position 396. Moreover, bilirubin is oxidized even in the absence of the Trp-His covalent bond, proving that its role in electron transfer is not crucial <ref name="struct"/>.

== Function ==

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@@ Line 22: / Line 22: @@
 =====Covalent bond between Trp396 and His398=====
-Since the discovery of bilirubin oxidase, two cristal structures of native enzyme have been published independently. The structure shown here and described by Cracknell ''et al.'' reveals that the imidazole ring of His398 —one of the T1Cu ligands — is abnormally close to the indole ring of Trp396, which raises the possibility that there is a <scene name='82/829357/Trp-his_covalent_bond/1'>His–Trp link</scene>. On the contrary in the structure described by Mizutani ''et al.'' (cf [[3abg]]) the indole ring of Trp396 turns away and does not form the covalent bond with the imidazole ring of His398 <ref name="stru">DOI: 10.1002/chem.201803798</ref>.
+Since the discovery of bilirubin oxidase, two cristal structures of native enzyme have been published independently. The structure shown here and described by Cracknell ''et al.'' reveals that the imidazole ring of His398 —one of the T1Cu ligands — is abnormally close to the indole ring of <scene name='82/829357/Trp396/1'>Trp396</scene>, which raises the possibility that there is a <scene name='82/829357/Trp-his_covalent_bond/1'>His–Trp link</scene>. On the contrary in the structure described by Mizutani ''et al.'' (cf [[3abg]]) the indole ring of <scene name='82/829357/Trp396/1'>Trp396</scene> turns away and does not form the covalent bond with the imidazole ring of His398 <ref name="stru">DOI: 10.1002/chem.201803798</ref>.
-Several studies proved that bilirubin oxidase has actually a post-translationally formed covalent bond between the imidazole ring of His398 coordinated to type I copper and the indole ring of Trp396 <ref name="stru"/><ref>DOI: 10.1016/j.bbrc.2019.10.159</ref><ref name="struct">DOI: 10.1038/s41598-019-50105-3</ref>. Indeed, the distance between Trp396 and His398 is 1.9 Å, which is shorter than the Van der Waals distance. Moreover, the torsion angle between the side chain rings of Trp396 and His398 is 65°, suggesting that the covalent link comprises a single bond <ref name="stru"/>.
+Several studies proved that bilirubin oxidase has actually a post-translationally formed covalent bond between the imidazole ring of His398 coordinated to type I copper and the indole ring of <scene name='82/829357/Trp396/1'>Trp396</scene> <ref name="stru"/><ref>DOI: 10.1016/j.bbrc.2019.10.159</ref><ref name="struct">DOI: 10.1038/s41598-019-50105-3</ref>. Indeed, the distance between <scene name='82/829357/Trp396/1'>Trp396</scene> and His398 is 1.9 Å, which is shorter than the Van der Waals distance. Moreover, the torsion angle between the side chain rings of <scene name='82/829357/Trp396/1'>Trp396</scene> and His398 is 65°, suggesting that the covalent link comprises a single bond <ref name="stru"/>.
-Among the multicopper oxidases, bilirubin oxidase is the only one which forms this <scene name='82/829357/Trp-his_covalent_bond/1'>His-Trp link</scene>. It is due to the particular molecular environment of the Trp396 residue, which is unique among the multicopper oxidases registered in the PDB. Indeed, the equivalent position is occupied by a glutamate side chain in multicopper oxidases from ''Thermus thermophilus'' ([[2xu9]]) and ''Campylobacter jejuni'' ([[3zx1]]), by aspartate in yeast Fet3p ([[1zpu]]), and by a main chain carbonyl oxygen atom in laccases from ''Antrodiella faginea'' ([[5ehf]]), ''Cerrena maxima'' ([[5h5u]]), ''Coriolus zonatus'' ([[2hzh]]), ''Lentinus sp.'' ([[3x1b]]), ''Lentinus tigrinus'' ([[2qt6]]), ''Steccherinum murashkinskyi'' ([[5mig]]), ''Trametes hirsuta'' ([[3fpx]]), and ''Trametes sp.'' AH28-2 ([[3kw7]]) <ref name="stru"/>.
+Among the multicopper oxidases, bilirubin oxidase is the only one which forms this <scene name='82/829357/Trp-his_covalent_bond/1'>His-Trp link</scene>. It is due to the particular molecular environment of the <scene name='82/829357/Trp396/1'>Trp396</scene> residue, which is unique among the multicopper oxidases registered in the PDB. Indeed, the equivalent position is occupied by a glutamate side chain in multicopper oxidases from ''Thermus thermophilus'' ([[2xu9]]) and ''Campylobacter jejuni'' ([[3zx1]]), by aspartate in yeast Fet3p ([[1zpu]]), and by a main chain carbonyl oxygen atom in laccases from ''Antrodiella faginea'' ([[5ehf]]), ''Cerrena maxima'' ([[5h5u]]), ''Coriolus zonatus'' ([[2hzh]]), ''Lentinus sp.'' ([[3x1b]]), ''Lentinus tigrinus'' ([[2qt6]]), ''Steccherinum murashkinskyi'' ([[5mig]]), ''Trametes hirsuta'' ([[3fpx]]), and ''Trametes sp.'' AH28-2 ([[3kw7]]) <ref name="stru"/>.
-The role of this covalent bond between the indole ring of Trp396 and the imidazole ring of His398 has been investigated using mutants of bilirubin oxidase (at the position 396). Their enzymatic activities have been compared with the one of wild type bilirubin oxidase. All the mutations have led to a significant decrease of the catalytic efficiency for bilirubin, compared to the wild type bilirubin oxidase. It proves that the <scene name='82/829357/Trp-his_covalent_bond/1'>Trp396-His398</scene> covalent bond has a major role in the enzymatic activity of bilirubin oxidase. However, it has no influence on the enzyme structure (except the replaced residue), since bilirubin can still bind to mutants not containing tryptophan at the position 396. Moreover, bilirubin is oxidized even in the absence of the Trp-His covalent bond, proving that its role in electron transfer is not crucial <ref name="struct"/>.
+The role of this covalent bond between the indole ring of <scene name='82/829357/Trp396/1'>Trp396</scene> and the imidazole ring of His398 has been investigated using mutants of bilirubin oxidase (at the position 396). Their enzymatic activities have been compared with the one of wild type bilirubin oxidase. All the mutations have led to a significant decrease of the catalytic efficiency for bilirubin, compared to the wild type bilirubin oxidase. It proves that the <scene name='82/829357/Trp-his_covalent_bond/1'>Trp396-His398</scene> covalent bond has a major role in the enzymatic activity of bilirubin oxidase. However, it has no influence on the enzyme structure (except the replaced residue), since bilirubin can still bind to mutants not containing tryptophan at the position 396. Moreover, bilirubin is oxidized even in the absence of the Trp-His covalent bond, proving that its role in electron transfer is not crucial <ref name="struct"/>.
 == Function ==