Hemeproteins - Revision history

Alexander Berchansky at 10:52, 22 July 2021

Alexander Berchansky — Thu, 22 Jul 2021 10:52:16 GMT

←Older revision		Revision as of 10:52, 22 July 2021
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	*[[Extremophile\|Elephant ''vs'' whale myoglobin]]		*[[Extremophile\|Elephant ''vs'' whale myoglobin]]
	=Ascorbate peroxidase=		=Ascorbate peroxidase=
-	== Function ==	+	Function

	'''Ascorbate peroxidase''' (APX) catalyzes the conversion of ascorbate and hydrogen peroxide to dehydroascorbate and water thus detoxifying hydrogen peroxide. APX is involved in the glutathione-ascorbate cycle. APX is accumulated in plants in response to heat and drought stress. APX contains a heme group.		'''Ascorbate peroxidase''' (APX) catalyzes the conversion of ascorbate and hydrogen peroxide to dehydroascorbate and water thus detoxifying hydrogen peroxide. APX is involved in the glutathione-ascorbate cycle. APX is accumulated in plants in response to heat and drought stress. APX contains a heme group.

-	== Relevance ==	+	Relevance

	APX is part of plants antioxidant defense. APX converts H2O2 to water using ascorbate as an electron donor. APX is used in electron microscopy as a genetic tag which can be stained independently of light activation.		APX is part of plants antioxidant defense. APX converts H2O2 to water using ascorbate as an electron donor. APX is used in electron microscopy as a genetic tag which can be stained independently of light activation.

-	== Structural highlights ==	+	Structural highlights

	The <scene name='48/486478/Cv/4'>heme-containing active site</scene> of APX contains a <scene name='48/486478/Cv/5'>His residue (H163 in soybean) which coordinates with the heme</scene> and confers stability to the Fe state in the heme. <ref>PMID:12640445</ref>		The <scene name='48/486478/Cv/4'>heme-containing active site</scene> of APX contains a <scene name='48/486478/Cv/5'>His residue (H163 in soybean) which coordinates with the heme</scene> and confers stability to the Fe state in the heme. <ref>PMID:12640445</ref>
		+
		+	=[[Journal:Acta Cryst D:S2059798320013510\|Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine-2,3-dioxygenase-1]]=
	</StructureSection>		</StructureSection>
	<b>References</b><br>		<b>References</b><br>

Alexander Berchansky at 15:00, 21 July 2021

Alexander Berchansky — Wed, 21 Jul 2021 15:00:47 GMT

←Older revision		Revision as of 15:00, 21 July 2021
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	===[[Cytochrome c 7]]===		===[[Cytochrome c 7]]===
		+
		+	===[[Journal:Acta Cryst D:S2059798320003101\|The crystal structure of heme ''d<sub>1</sub>'' biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states ''in crystallo'']]===

	===For details on decaheme cyt see [[MtrF]]===		===For details on decaheme cyt see [[MtrF]]===

Alexander Berchansky at 15:58, 25 February 2020

Alexander Berchansky — Tue, 25 Feb 2020 15:58:21 GMT

←Older revision		Revision as of 15:58, 25 February 2020
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	The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>		The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>
		+
		+	==[[Flavocytochrome]]==

	=Cytochrome c Nitrite Reductase=		=Cytochrome c Nitrite Reductase=

Alexander Berchansky at 13:58, 28 January 2020

Alexander Berchansky — Tue, 28 Jan 2020 13:58:23 GMT

←Older revision		Revision as of 13:58, 28 January 2020
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	=[[Myoglobin]]=		=[[Myoglobin]]=
	*[[Extremophile\|Elephant ''vs'' whale myoglobin]]		*[[Extremophile\|Elephant ''vs'' whale myoglobin]]
		+	=Ascorbate peroxidase=
		+	== Function ==
		+
		+	'''Ascorbate peroxidase''' (APX) catalyzes the conversion of ascorbate and hydrogen peroxide to dehydroascorbate and water thus detoxifying hydrogen peroxide. APX is involved in the glutathione-ascorbate cycle. APX is accumulated in plants in response to heat and drought stress. APX contains a heme group.
		+
		+	== Relevance ==
		+
		+	APX is part of plants antioxidant defense. APX converts H2O2 to water using ascorbate as an electron donor. APX is used in electron microscopy as a genetic tag which can be stained independently of light activation.
		+
		+	== Structural highlights ==
		+
		+	The <scene name='48/486478/Cv/4'>heme-containing active site</scene> of APX contains a <scene name='48/486478/Cv/5'>His residue (H163 in soybean) which coordinates with the heme</scene> and confers stability to the Fe state in the heme. <ref>PMID:12640445</ref>
	</StructureSection>		</StructureSection>
	<b>References</b><br>		<b>References</b><br>

Alexander Berchansky at 13:15, 13 January 2020

Alexander Berchansky — Mon, 13 Jan 2020 13:15:29 GMT

←Older revision		Revision as of 13:15, 13 January 2020
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	=Cytochrome c Nitrite Reductase=		=Cytochrome c Nitrite Reductase=
-		+	== ''Shewanella oneidensis'' Cytochrome c Nitrite Reductase ==
	[[Journal:JBIC:16\|Laue Crystal Structure of ''Shewanella oneidensis'' Cytochrome c Nitrite Reductase from a High-yield Expression System]]<ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>		[[Journal:JBIC:16\|Laue Crystal Structure of ''Shewanella oneidensis'' Cytochrome c Nitrite Reductase from a High-yield Expression System]]<ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>
	Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.		Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.
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	[[Image:figur5.jpg\|left\|378px\|thumb\|PFV of ''S. oneidensis'' ccNiR (a) Typical signal on a graphite electrode. (b) Baselinesubtracted non-turnover voltammogram]]		[[Image:figur5.jpg\|left\|378px\|thumb\|PFV of ''S. oneidensis'' ccNiR (a) Typical signal on a graphite electrode. (b) Baselinesubtracted non-turnover voltammogram]]
	The Ca<sup>2+</sup> ion within <scene name='Journal:JBIC:16/Cv/14'>conserved site</scene> is coordinated in bidentate fashion by <scene name='Journal:JBIC:16/Cv/15'>Glu205</scene>, and in monodentate fashion by the <scene name='Journal:JBIC:16/Cv/16'>Tyr206 and Lys254</scene> backbone carbonyls, and the <scene name='Journal:JBIC:16/Cv/17'>Gln256</scene> side-chain carbonyl. In the ''S. oneidensis'' structure only <scene name='Journal:JBIC:16/Cv/18'>one water molecule</scene> is assigned to the Ca<sup>2+</sup> ion in subunit B. In subunit A the difference electron density that represents this water molecule is very close to the noise level, and it is difficult to identify even one water molecule there. The <scene name='Journal:JBIC:16/Cv/14'>carbonyl side chain of Asp242 and the hydroxyl of Tyr235</scene> come near to the open calcium coordination sites, but are not within bonding distance. Instead they interact with the water molecule that is weakly coordinated to the Ca<sup>2+</sup> ion. The ccNiR calcium ions appear to play a vital role in organizing the <scene name='Journal:JBIC:16/Cv/13'>active site</scene> (as was mentioned above <font color='magenta'><b>hemes-1</b></font> are the active sites).		The Ca<sup>2+</sup> ion within <scene name='Journal:JBIC:16/Cv/14'>conserved site</scene> is coordinated in bidentate fashion by <scene name='Journal:JBIC:16/Cv/15'>Glu205</scene>, and in monodentate fashion by the <scene name='Journal:JBIC:16/Cv/16'>Tyr206 and Lys254</scene> backbone carbonyls, and the <scene name='Journal:JBIC:16/Cv/17'>Gln256</scene> side-chain carbonyl. In the ''S. oneidensis'' structure only <scene name='Journal:JBIC:16/Cv/18'>one water molecule</scene> is assigned to the Ca<sup>2+</sup> ion in subunit B. In subunit A the difference electron density that represents this water molecule is very close to the noise level, and it is difficult to identify even one water molecule there. The <scene name='Journal:JBIC:16/Cv/14'>carbonyl side chain of Asp242 and the hydroxyl of Tyr235</scene> come near to the open calcium coordination sites, but are not within bonding distance. Instead they interact with the water molecule that is weakly coordinated to the Ca<sup>2+</sup> ion. The ccNiR calcium ions appear to play a vital role in organizing the <scene name='Journal:JBIC:16/Cv/13'>active site</scene> (as was mentioned above <font color='magenta'><b>hemes-1</b></font> are the active sites).
		+
		+	==[[Cytochrome c nitrite reductase]]==

	=Cytochrome c oxidase=		=Cytochrome c oxidase=

Alexander Berchansky at 13:11, 13 January 2020

Alexander Berchansky — Mon, 13 Jan 2020 13:11:21 GMT

←Older revision		Revision as of 13:11, 13 January 2020
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	The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>		The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>

-	=Cytochrome c Nitrite Reductase~~<ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>~~=	+	=Cytochrome c Nitrite Reductase=

		+	[[Journal:JBIC:16\|Laue Crystal Structure of ''Shewanella oneidensis'' Cytochrome c Nitrite Reductase from a High-yield Expression System]]<ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>
	Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.		Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.
	The ccNiR described here is produced by the ''Shewanella oneidensis'' bacterium, which is remarkable in its own right due to the large number of electron acceptors that it can utilize. ''Shewanella'' is a facultative anaerobe, which means that it will use oxygen if available, but in the absence of oxygen can get rid of its electrons by dumping them on a wide range of alternate acceptors, of which nitrite is only one example. To handle the electron flow ''Shewanella'' uses a large number of promiscuous <scene name='Journal:JBIC:16/Cv/8'>c-heme</scene> containing electron transfer proteins. Indeed, ''Shewanella'' is exceptionally adept at producing c-heme proteins under fast-growth conditions, which many bacteria commonly used for large-scale laboratory gene expression, such as ''E. coli'', are incapable of unless they are first extensively reprogrammed genetically. Since ''Shewanella'' can be easily grown in the lab, and can naturally and easily produce c-hemes, it is an ideal host for generating large quantities of c-heme proteins such as ccNiR.		The ccNiR described here is produced by the ''Shewanella oneidensis'' bacterium, which is remarkable in its own right due to the large number of electron acceptors that it can utilize. ''Shewanella'' is a facultative anaerobe, which means that it will use oxygen if available, but in the absence of oxygen can get rid of its electrons by dumping them on a wide range of alternate acceptors, of which nitrite is only one example. To handle the electron flow ''Shewanella'' uses a large number of promiscuous <scene name='Journal:JBIC:16/Cv/8'>c-heme</scene> containing electron transfer proteins. Indeed, ''Shewanella'' is exceptionally adept at producing c-heme proteins under fast-growth conditions, which many bacteria commonly used for large-scale laboratory gene expression, such as ''E. coli'', are incapable of unless they are first extensively reprogrammed genetically. Since ''Shewanella'' can be easily grown in the lab, and can naturally and easily produce c-hemes, it is an ideal host for generating large quantities of c-heme proteins such as ccNiR.

Alexander Berchansky at 13:08, 13 January 2020

Alexander Berchansky — Mon, 13 Jan 2020 13:08:06 GMT

←Older revision		Revision as of 13:08, 13 January 2020
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	The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>		The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>

-	=Cytochrome c Nitrite Reductase= <ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>	+	=Cytochrome c Nitrite Reductase<ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>=

	Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.		Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.

Alexander Berchansky at 13:07, 13 January 2020

Alexander Berchansky — Mon, 13 Jan 2020 13:07:06 GMT

←Older revision		Revision as of 13:07, 13 January 2020
Line 104:		Line 104:
	The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>		The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>

-	=Cytochrome c Nitrite Reductase=<ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>	+	=Cytochrome c Nitrite Reductase= <ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>

	Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.		Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.

Alexander Berchansky at 13:05, 13 January 2020

Alexander Berchansky — Mon, 13 Jan 2020 13:05:32 GMT

←Older revision		Revision as of 13:05, 13 January 2020
Line 104:		Line 104:
	The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>		The <scene name='43/430105/Cv/6'>heme moiety is stabilized by several side chains</scene>. The <scene name='43/430105/Cv/7'>heme iron is pentacoordinated with Cys as one ligand</scene>.<ref>PMID:12861225</ref>

-	=Cytochrome c Nitrite Reductase<ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>=	+	=Cytochrome c Nitrite Reductase=<ref name="Youngblut">doi 10.1007/s00775-012-0885-0</ref>

	Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.		Cytochrome c nitrite reductase (ccNIR) is a central enzyme of the nitrogen cycle. It binds nitrite, and reduces it by transferring 6 electrons to form ammonia. This ammonia can then be utilized to synthesize nitrogen containing molecules such as amino acids or nucleic acids. However, ccNiR’s primary role is to help extract energy from the reduction; ammonia is simply a potentially useful byproduct. In general, heterotrophic organisms feed on electron-rich substances such as sugars or fatty acids. During the metabolism of these substances large numbers of electrons are produced. Many organisms use oxygen as the final acceptor of these electrons, in which case water is formed. However, some organisms can use alternative electron acceptors such as nitrite, which is where ccNiR comes in.

Alexander Berchansky at 13:42, 3 December 2019

Alexander Berchansky — Tue, 03 Dec 2019 13:42:12 GMT

←Older revision		Revision as of 13:42, 3 December 2019
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	*<scene name='77/774654/Cv/8'>Fe coordination site</scene>.		*<scene name='77/774654/Cv/8'>Fe coordination site</scene>.
	*<scene name='77/774654/Cv/9'>Distances between Lauric acid oxygens and heme group Fe</scene> in Cytochrome P450 hydroxylase from ''Steptomyces avermitilis'' (PDB code [[5cwe]]).		*<scene name='77/774654/Cv/9'>Distances between Lauric acid oxygens and heme group Fe</scene> in Cytochrome P450 hydroxylase from ''Steptomyces avermitilis'' (PDB code [[5cwe]]).
		+	=[[Heme oxygenase]]=
	=[[Hemoglobin]]=		=[[Hemoglobin]]=
	=[[Myoglobin]]=		=[[Myoglobin]]=