Nitrotyrosine - Revision history

Eric Martz at 20:35, 19 March 2011

Eric Martz — Sat, 19 Mar 2011 20:35:59 GMT

←Older revision		Revision as of 20:35, 19 March 2011
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	In March, 2011, there are 13 entries in the [[PDB]] containing coordinates for 3-nitrotyrosine (meta-nitro-tyrosine), with the [[Non-Standard_Residues\|compound ID]] '''NIY'''. These include six sequence-distinct proteins, represented by ribonucleotide reductase [[2xof]] and [[2xap]], laccase [[3div]], Human Manganese Superoxide Dismutase [[2adp]], Human Glutathione Reductase [[1k4q]], and bovine Cu,Zn superoxide dismutase [[1sda]]. Not surprisingly, the NO<sub>2</sub> adduct, being very hydrophilic, is often on the surface of the protein.		In March, 2011, there are 13 entries in the [[PDB]] containing coordinates for 3-nitrotyrosine (meta-nitro-tyrosine), with the [[Non-Standard_Residues\|compound ID]] '''NIY'''. These include six sequence-distinct proteins, represented by ribonucleotide reductase [[2xof]] and [[2xap]], laccase [[3div]], Human Manganese Superoxide Dismutase [[2adp]], Human Glutathione Reductase [[1k4q]], and bovine Cu,Zn superoxide dismutase [[1sda]]. Not surprisingly, the NO<sub>2</sub> adduct, being very hydrophilic, is often on the surface of the protein.
	{{Clear}}		{{Clear}}
-	<Structure size='450' frame='true' align='right' caption='' ~~scene='Insert optional scene name here'~~	+	<Structure size='450' frame='true' align='right' caption='' scene='Sandbox7_Eric_Martz/Cartoon/1' />
-	scene='Sandbox7_Eric_Martz/Cartoon/1' />	+
	One interesting case is Human <font color="#00c000">'''Manganese'''</font> Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, <font color="#00c000">'''Mn<sup>++</sup>'''</font> is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The <font color="#00c000">'''Mn<sup>++</sup>'''</font> is		One interesting case is Human <font color="#00c000">'''Manganese'''</font> Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, <font color="#00c000">'''Mn<sup>++</sup>'''</font> is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The <font color="#00c000">'''Mn<sup>++</sup>'''</font> is
	<scene name='Sandbox7_Eric_Martz/Mn_contacts/1'>caged</scene> by four histidine <font color="#3050F8">'''nitrogens'''</font>, one aspartate <font color="#ff0d0d">'''oxygen'''</font>, and one <font color="magenta">'''water'''</font>. Tyrosine 34 is nearby (5.2 Ångstroms), but not near enough to be interacting with the <font color="#00c000">'''Mn<sup>++</sup>'''</font> or its cage.		<scene name='Sandbox7_Eric_Martz/Mn_contacts/1'>caged</scene> by four histidine <font color="#3050F8">'''nitrogens'''</font>, one aspartate <font color="#ff0d0d">'''oxygen'''</font>, and one <font color="magenta">'''water'''</font>. Tyrosine 34 is nearby (5.2 Ångstroms), but not near enough to be interacting with the <font color="#00c000">'''Mn<sup>++</sup>'''</font> or its cage.

Eric Martz at 20:35, 19 March 2011

Eric Martz — Sat, 19 Mar 2011 20:35:22 GMT

←Older revision		Revision as of 20:35, 19 March 2011
Line 4:		Line 4:
	In March, 2011, there are 13 entries in the [[PDB]] containing coordinates for 3-nitrotyrosine (meta-nitro-tyrosine), with the [[Non-Standard_Residues\|compound ID]] '''NIY'''. These include six sequence-distinct proteins, represented by ribonucleotide reductase [[2xof]] and [[2xap]], laccase [[3div]], Human Manganese Superoxide Dismutase [[2adp]], Human Glutathione Reductase [[1k4q]], and bovine Cu,Zn superoxide dismutase [[1sda]]. Not surprisingly, the NO<sub>2</sub> adduct, being very hydrophilic, is often on the surface of the protein.		In March, 2011, there are 13 entries in the [[PDB]] containing coordinates for 3-nitrotyrosine (meta-nitro-tyrosine), with the [[Non-Standard_Residues\|compound ID]] '''NIY'''. These include six sequence-distinct proteins, represented by ribonucleotide reductase [[2xof]] and [[2xap]], laccase [[3div]], Human Manganese Superoxide Dismutase [[2adp]], Human Glutathione Reductase [[1k4q]], and bovine Cu,Zn superoxide dismutase [[1sda]]. Not surprisingly, the NO<sub>2</sub> adduct, being very hydrophilic, is often on the surface of the protein.
	{{Clear}}		{{Clear}}
-	<Structure size='450' frame='true' align='right' caption='~~Insert caption here~~' scene='Insert optional scene name here'	+	<Structure size='450' frame='true' align='right' caption='' scene='Insert optional scene name here'
	scene='Sandbox7_Eric_Martz/Cartoon/1' />		scene='Sandbox7_Eric_Martz/Cartoon/1' />
	One interesting case is Human <font color="#00c000">'''Manganese'''</font> Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, <font color="#00c000">'''Mn<sup>++</sup>'''</font> is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The <font color="#00c000">'''Mn<sup>++</sup>'''</font> is		One interesting case is Human <font color="#00c000">'''Manganese'''</font> Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, <font color="#00c000">'''Mn<sup>++</sup>'''</font> is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The <font color="#00c000">'''Mn<sup>++</sup>'''</font> is

Eric Martz at 22:15, 18 March 2011

Eric Martz — Fri, 18 Mar 2011 22:15:04 GMT

←Older revision		Revision as of 22:15, 18 March 2011
Line 2:		Line 2:
	Nitrotyrosine<ref>[[User:Eric Martz]] wishes to thank [http://www.cancer.ucla.edu/index.aspx?page=645&recordid=338 Hermes J. Garbán] for bringing nitrotyrosine to his attention.</ref> results from the post-translational modification of the [[Amino_Acids\|standard amino acid]] tyrosine. Reactive nitrogen compounds produced in inflammation are typically responsible. Nitrosylation of tyrosine tends to inactivate enzymes.		Nitrotyrosine<ref>[[User:Eric Martz]] wishes to thank [http://www.cancer.ucla.edu/index.aspx?page=645&recordid=338 Hermes J. Garbán] for bringing nitrotyrosine to his attention.</ref> results from the post-translational modification of the [[Amino_Acids\|standard amino acid]] tyrosine. Reactive nitrogen compounds produced in inflammation are typically responsible. Nitrosylation of tyrosine tends to inactivate enzymes.

-	In March, 2011, there are 13 entries in the [[PDB]] containing coordinates for 3-nitrotyrosine (meta-nitro-tyrosine), with the [[~~http://www.proteopedia.org/wiki/index.php/~~Non-Standard_Residues\|compound ID]] '''NIY'''. These include six sequence-distinct proteins, represented by ribonucleotide reductase [[2xof]] and [[2xap]], laccase [[3div]], Human Manganese Superoxide Dismutase [[2adp]], Human Glutathione Reductase [[1k4q]], and bovine Cu,Zn superoxide dismutase [[1sda]]. Not surprisingly, the NO<sub>2</sub> adduct, being very hydrophilic, is often on the surface of the protein.	+	In March, 2011, there are 13 entries in the [[PDB]] containing coordinates for 3-nitrotyrosine (meta-nitro-tyrosine), with the [[Non-Standard_Residues\|compound ID]] '''NIY'''. These include six sequence-distinct proteins, represented by ribonucleotide reductase [[2xof]] and [[2xap]], laccase [[3div]], Human Manganese Superoxide Dismutase [[2adp]], Human Glutathione Reductase [[1k4q]], and bovine Cu,Zn superoxide dismutase [[1sda]]. Not surprisingly, the NO<sub>2</sub> adduct, being very hydrophilic, is often on the surface of the protein.
	{{Clear}}		{{Clear}}
	<Structure size='450' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here'		<Structure size='450' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here'

Eric Martz at 21:32, 18 March 2011

Eric Martz — Fri, 18 Mar 2011 21:32:23 GMT

←Older revision		Revision as of 21:32, 18 March 2011
Line 6:		Line 6:
	<Structure size='450' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here'		<Structure size='450' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here'
	scene='Sandbox7_Eric_Martz/Cartoon/1' />		scene='Sandbox7_Eric_Martz/Cartoon/1' />
-	One interesting case is Human <font color="#00c000">'''Manganese'''</font> Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, <font color="#00c000">'''Mn<sup>++</sup>'''</font> is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The is	+	One interesting case is Human <font color="#00c000">'''Manganese'''</font> Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, <font color="#00c000">'''Mn<sup>++</sup>'''</font> is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The <font color="#00c000">'''Mn<sup>++</sup>'''</font> is
	<scene name='Sandbox7_Eric_Martz/Mn_contacts/1'>caged</scene> by four histidine <font color="#3050F8">'''nitrogens'''</font>, one aspartate <font color="#ff0d0d">'''oxygen'''</font>, and one <font color="magenta">'''water'''</font>. Tyrosine 34 is nearby (5.2 Ångstroms), but not near enough to be interacting with the <font color="#00c000">'''Mn<sup>++</sup>'''</font> or its cage.		<scene name='Sandbox7_Eric_Martz/Mn_contacts/1'>caged</scene> by four histidine <font color="#3050F8">'''nitrogens'''</font>, one aspartate <font color="#ff0d0d">'''oxygen'''</font>, and one <font color="magenta">'''water'''</font>. Tyrosine 34 is nearby (5.2 Ångstroms), but not near enough to be interacting with the <font color="#00c000">'''Mn<sup>++</sup>'''</font> or its cage.
	<scene name='Sandbox7_Eric_Martz/Contacts_to_nitrotyrosine/1'>Nitrosylation of tyrosine 34</scene> extends it towards the <font color="#00c000">'''Mn<sup>++</sup>'''</font>. The partially negatively charged <font color="#ff0d0d">'''oxygens'''</font> in the NO<sub>2</sub> are 3.6-3.8 Å from the electron-hungry <font color="#00c000">'''Mn<sup>++</sup>'''</font>. <scene name='Sandbox7_Eric_Martz/Aligned_pre_and_post_nitro/2'>Nitrosylation pushes the tyrosine ring</scene> slightly farther from the <font color="#00c000">'''Mn<sup>++</sup>'''</font>, but causes no other significant conformational changes<ref>[[DeepView]] was used to align all atoms of the three Mn-coordinating histidines. In the resulting file [[Image:2adq-2adp-3hisaln.pdb]], 2adq is model 1, and 2adp is model 2.</ref>. The authors<ref>PMID: 16443160</ref> conclude		<scene name='Sandbox7_Eric_Martz/Contacts_to_nitrotyrosine/1'>Nitrosylation of tyrosine 34</scene> extends it towards the <font color="#00c000">'''Mn<sup>++</sup>'''</font>. The partially negatively charged <font color="#ff0d0d">'''oxygens'''</font> in the NO<sub>2</sub> are 3.6-3.8 Å from the electron-hungry <font color="#00c000">'''Mn<sup>++</sup>'''</font>. <scene name='Sandbox7_Eric_Martz/Aligned_pre_and_post_nitro/2'>Nitrosylation pushes the tyrosine ring</scene> slightly farther from the <font color="#00c000">'''Mn<sup>++</sup>'''</font>, but causes no other significant conformational changes<ref>[[DeepView]] was used to align all atoms of the three Mn-coordinating histidines. In the resulting file [[Image:2adq-2adp-3hisaln.pdb]], 2adq is model 1, and 2adp is model 2.</ref>. The authors<ref>PMID: 16443160</ref> conclude

Eric Martz at 21:31, 18 March 2011

Eric Martz — Fri, 18 Mar 2011 21:31:54 GMT

←Older revision		Revision as of 21:31, 18 March 2011
Line 6:		Line 6:
	<Structure size='450' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here'		<Structure size='450' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here'
	scene='Sandbox7_Eric_Martz/Cartoon/1' />		scene='Sandbox7_Eric_Martz/Cartoon/1' />
-	One ~~of the more~~ interesting ~~cases may be~~ Human <font color="#00c000">'''Manganese'''</font> Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, <font color="#00c000">'''Mn<sup>++</sup>'''</font> is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The is	+	One interesting case is Human <font color="#00c000">'''Manganese'''</font> Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, <font color="#00c000">'''Mn<sup>++</sup>'''</font> is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The is
	<scene name='Sandbox7_Eric_Martz/Mn_contacts/1'>caged</scene> by four histidine <font color="#3050F8">'''nitrogens'''</font>, one aspartate <font color="#ff0d0d">'''oxygen'''</font>, and one <font color="magenta">'''water'''</font>. Tyrosine 34 is nearby (5.2 Ångstroms), but not near enough to be interacting with the <font color="#00c000">'''Mn<sup>++</sup>'''</font> or its cage.		<scene name='Sandbox7_Eric_Martz/Mn_contacts/1'>caged</scene> by four histidine <font color="#3050F8">'''nitrogens'''</font>, one aspartate <font color="#ff0d0d">'''oxygen'''</font>, and one <font color="magenta">'''water'''</font>. Tyrosine 34 is nearby (5.2 Ångstroms), but not near enough to be interacting with the <font color="#00c000">'''Mn<sup>++</sup>'''</font> or its cage.
	<scene name='Sandbox7_Eric_Martz/Contacts_to_nitrotyrosine/1'>Nitrosylation of tyrosine 34</scene> extends it towards the <font color="#00c000">'''Mn<sup>++</sup>'''</font>. The partially negatively charged <font color="#ff0d0d">'''oxygens'''</font> in the NO<sub>2</sub> are 3.6-3.8 Å from the electron-hungry <font color="#00c000">'''Mn<sup>++</sup>'''</font>. <scene name='Sandbox7_Eric_Martz/Aligned_pre_and_post_nitro/2'>Nitrosylation pushes the tyrosine ring</scene> slightly farther from the <font color="#00c000">'''Mn<sup>++</sup>'''</font>, but causes no other significant conformational changes<ref>[[DeepView]] was used to align all atoms of the three Mn-coordinating histidines. In the resulting file [[Image:2adq-2adp-3hisaln.pdb]], 2adq is model 1, and 2adp is model 2.</ref>. The authors<ref>PMID: 16443160</ref> conclude		<scene name='Sandbox7_Eric_Martz/Contacts_to_nitrotyrosine/1'>Nitrosylation of tyrosine 34</scene> extends it towards the <font color="#00c000">'''Mn<sup>++</sup>'''</font>. The partially negatively charged <font color="#ff0d0d">'''oxygens'''</font> in the NO<sub>2</sub> are 3.6-3.8 Å from the electron-hungry <font color="#00c000">'''Mn<sup>++</sup>'''</font>. <scene name='Sandbox7_Eric_Martz/Aligned_pre_and_post_nitro/2'>Nitrosylation pushes the tyrosine ring</scene> slightly farther from the <font color="#00c000">'''Mn<sup>++</sup>'''</font>, but causes no other significant conformational changes<ref>[[DeepView]] was used to align all atoms of the three Mn-coordinating histidines. In the resulting file [[Image:2adq-2adp-3hisaln.pdb]], 2adq is model 1, and 2adp is model 2.</ref>. The authors<ref>PMID: 16443160</ref> conclude

Eric Martz at 21:30, 18 March 2011

Eric Martz — Fri, 18 Mar 2011 21:30:36 GMT

←Older revision		Revision as of 21:30, 18 March 2011
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-	Proposed Title: <span style="font-size:150%">'''Nitrotyrosine.'''</span>
-	<center><table cellpadding="8" border="1" width="90%" style="background: #ffe0b0;"><tr><td>
-	This page is reserved for a collaboration between [[User:Eric Martz]] and [http://www.cancer.ucla.edu/index.aspx?page=645&recordid=338 Hermes J Garbán].
-	</td></tr></table></center>
-
	[[Image:800px-Nitrotyrosine.png\|right\|thumb\|3-Nitrotyrosine]]		[[Image:800px-Nitrotyrosine.png\|right\|thumb\|3-Nitrotyrosine]]
	Nitrotyrosine<ref>[[User:Eric Martz]] wishes to thank [http://www.cancer.ucla.edu/index.aspx?page=645&recordid=338 Hermes J. Garbán] for bringing nitrotyrosine to his attention.</ref> results from the post-translational modification of the [[Amino_Acids\|standard amino acid]] tyrosine. Reactive nitrogen compounds produced in inflammation are typically responsible. Nitrosylation of tyrosine tends to inactivate enzymes.		Nitrotyrosine<ref>[[User:Eric Martz]] wishes to thank [http://www.cancer.ucla.edu/index.aspx?page=645&recordid=338 Hermes J. Garbán] for bringing nitrotyrosine to his attention.</ref> results from the post-translational modification of the [[Amino_Acids\|standard amino acid]] tyrosine. Reactive nitrogen compounds produced in inflammation are typically responsible. Nitrosylation of tyrosine tends to inactivate enzymes.

Eric Martz: Created page

Eric Martz — Fri, 18 Mar 2011 21:30:16 GMT

Created page

New page

Proposed Title: '''Nitrotyrosine.'''
<center><table cellpadding="8" border="1" width="90%" style="background: #ffe0b0;"><tr><td>
This page is reserved for a collaboration between [[User:Eric Martz]] and [http://www.cancer.ucla.edu/index.aspx?page=645&recordid=338 Hermes J Garbán].
</td></tr></table></center>

[[Image:800px-Nitrotyrosine.png|right|thumb|3-Nitrotyrosine]]
Nitrotyrosine<ref>[[User:Eric Martz]] wishes to thank [http://www.cancer.ucla.edu/index.aspx?page=645&recordid=338 Hermes J. Garbán] for bringing nitrotyrosine to his attention.</ref> results from the post-translational modification of the [[Amino_Acids|standard amino acid]] tyrosine. Reactive nitrogen compounds produced in inflammation are typically responsible. Nitrosylation of tyrosine tends to inactivate enzymes.

In March, 2011, there are 13 entries in the [[PDB]] containing coordinates for 3-nitrotyrosine (meta-nitro-tyrosine), with the [[http://www.proteopedia.org/wiki/index.php/Non-Standard_Residues|compound ID]] '''NIY'''. These include six sequence-distinct proteins, represented by ribonucleotide reductase [[2xof]] and [[2xap]], laccase [[3div]], Human Manganese Superoxide Dismutase [[2adp]], Human Glutathione Reductase [[1k4q]], and bovine Cu,Zn superoxide dismutase [[1sda]]. Not surprisingly, the NO2 adduct, being very hydrophilic, is often on the surface of the protein.
{{Clear}}
<Structure size='450' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here'
scene='Sandbox7_Eric_Martz/Cartoon/1' />
One of the more interesting cases may be Human '''Manganese''' Superoxide Dismutase, for which structures are available for the wild type [[2adq]], shown at right (<scene name='Sandbox7_Eric_Martz/Cartoon/1'>restore initial scene</scene>), and the nitrated form, [[2adp]]. In this structure, '''Mn++''' is <scene name='Sandbox7_Eric_Martz/Cartoon/2'>buried</scene>. The is
<scene name='Sandbox7_Eric_Martz/Mn_contacts/1'>caged</scene> by four histidine '''nitrogens''', one aspartate '''oxygen''', and one '''water'''. Tyrosine 34 is nearby (5.2 Ångstroms), but not near enough to be interacting with the '''Mn++''' or its cage.
<scene name='Sandbox7_Eric_Martz/Contacts_to_nitrotyrosine/1'>Nitrosylation of tyrosine 34</scene> extends it towards the '''Mn++'''. The partially negatively charged '''oxygens''' in the NO2 are 3.6-3.8 Å from the electron-hungry '''Mn++'''. <scene name='Sandbox7_Eric_Martz/Aligned_pre_and_post_nitro/2'>Nitrosylation pushes the tyrosine ring</scene> slightly farther from the '''Mn++''', but causes no other significant conformational changes<ref>[[DeepView]] was used to align all atoms of the three Mn-coordinating histidines. In the resulting file [[Image:2adq-2adp-3hisaln.pdb]], 2adq is model 1, and 2adp is model 2.</ref>. The authors<ref>PMID: 16443160</ref> conclude
<blockquote>
"Inhibition of catalysis can be attributed to a steric effect of 3-nitrotyrosine 34 that impedes substrate access and binding, and alteration of the hydrogen-bond network that supports proton transfer in catalysis. It is also possible that an electrostatic effect of the nitro group has altered the finely tuned redox potential necessary for efficient catalysis, although the redox potential of nitrated MnSOD has not been measured."
</blockquote>

==See Also==
* [http://en.wikipedia.org/wiki/Nitrotyrosine Nitrotyrosine] in Wikipedia.

==Notes==
<references />