Sulfide quinone oxidoreductase
From Proteopedia
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==Introduction to SQOR== | ==Introduction to SQOR== | ||
| - | Oxidoreductases are used to catalyze the movement of electrons between an oxidant and a reductant. Sulfide quinone oxidoreductase, <scene name='88/881543/Sqor_-_1/1'>SQOR</scene>, is an integral membrane protein used in the mitochondria during metabolism to oxidize hydrogen sulfide with assistance from a quinone <ref name="jackson 1">PMID:30905673</ref>. This enzyme marks the committed step of the sulfide oxidation pathway. SQOR is also the enzyme involved in the irreversible step of hydrogen sulfide metabolism <ref name="landry">PMID:31591036</ref>. In the environment, sulfide is found in aquatic marine environments and in soil but is typically produced by prokaryotes and eukaryotes through catabolism <ref name="lencina">PMID:23103448</ref>. SQOR uses coenzyme Q as the electron acceptor, and it uses sulfide, sulfite, cyanide, or glutathione as a sulfane acceptor <ref name="SQOR-1">PMID:22852582</ref>. Sulfane, or thiosulfoxide sulfur, is an essential molecule in the regulation of cellular processes. It has the capabilities to create cofactors as well as modify enzymatic activities <ref name="toohey">PMID:25153879</ref>. Coenzyme Q is essential for electron transfer in metabolic processes, anabolic and catabolic. In bacterial SQOR, cytochrome C is used as the electron acceptor <ref name="jackson 1" />. The gasotransmitter, hydrogen sulfide or H2S, acts in biological processes and can be used as a target in drug interactions, which can be observed in mitochondrial metabolism <ref name="jackson 1">PMID:30905673</ref>. Hydrogen sulfide signaling is used in the cardiovascular system to prevent the development of cardiovascular diseases, such as hypertension <ref name="jackson 1"/>. SQOR can also be found in bacteria, producing sulfane sulfur metabolites <ref name="jackson 1">PMID:30905673</ref>. In contrast to human SQOR, it does not use a sulfane acceptor. In humans, SQOR belongs to the flavoprotein disulfide reductase (FDR) family (Miller, 2013). SQOR is also in the pyridine nucleotide- disulfide oxidoreductase family. There are also various types of SQORs found, such as SqrA, SqrB, SqrC, SqrD, SqrE, and SqrF <ref name="lencina">PMID:23103448</ref>. The crystallization method used on this SQOR was vapor diffusion at a pH of 7, which in result, gave indicators of the length and structure of this monumental enzyme. | + | Oxidoreductases are used to catalyze the movement of electrons between an oxidant and a reductant. '''Sulfide quinone oxidoreductase''' or '''Sulfide:quinone oxidoreductase''', <scene name='88/881543/Sqor_-_1/1'>SQOR</scene>, is an integral membrane protein used in the mitochondria during metabolism to oxidize hydrogen sulfide with assistance from a quinone <ref name="jackson 1">PMID:30905673</ref>. This enzyme marks the committed step of the sulfide oxidation pathway. SQOR is also the enzyme involved in the irreversible step of hydrogen sulfide metabolism <ref name="landry">PMID:31591036</ref>. In the environment, sulfide is found in aquatic marine environments and in soil but is typically produced by prokaryotes and eukaryotes through catabolism <ref name="lencina">PMID:23103448</ref>. SQOR uses coenzyme Q as the electron acceptor, and it uses sulfide, sulfite, cyanide, or glutathione as a sulfane acceptor <ref name="SQOR-1">PMID:22852582</ref>. Sulfane, or thiosulfoxide sulfur, is an essential molecule in the regulation of cellular processes. It has the capabilities to create cofactors as well as modify enzymatic activities <ref name="toohey">PMID:25153879</ref>. Coenzyme Q is essential for electron transfer in metabolic processes, anabolic and catabolic. In bacterial SQOR, cytochrome C is used as the electron acceptor <ref name="jackson 1" />. The gasotransmitter, hydrogen sulfide or H2S, acts in biological processes and can be used as a target in drug interactions, which can be observed in mitochondrial metabolism <ref name="jackson 1">PMID:30905673</ref>. Hydrogen sulfide signaling is used in the cardiovascular system to prevent the development of cardiovascular diseases, such as hypertension <ref name="jackson 1"/>. SQOR can also be found in bacteria, producing sulfane sulfur metabolites <ref name="jackson 1">PMID:30905673</ref>. In contrast to human SQOR, it does not use a sulfane acceptor. In humans, SQOR belongs to the flavoprotein disulfide reductase (FDR) family (Miller, 2013). SQOR is also in the pyridine nucleotide- disulfide oxidoreductase family. There are also various types of SQORs found, such as SqrA, SqrB, SqrC, SqrD, SqrE, and SqrF <ref name="lencina">PMID:23103448</ref>. The crystallization method used on this SQOR was vapor diffusion at a pH of 7, which in result, gave indicators of the length and structure of this monumental enzyme. |
| - | <StructureSection load='6oi5' size='340' side='right' caption=' | + | <StructureSection load='6oi5' size='340' side='right' caption='Human sulphide quinone oxidoreductase complex with FAD (PDB code [[6oi5]])' scene=''> |
This is the structure of Sulfide Quinone Oxidoreductase. '''Structure of Human Sulfide Quinone Oxidoreductase'''. | This is the structure of Sulfide Quinone Oxidoreductase. '''Structure of Human Sulfide Quinone Oxidoreductase'''. | ||
This page makes use of Jsmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> and Jmol <ref>PMID:21638687</ref>. | This page makes use of Jsmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> and Jmol <ref>PMID:21638687</ref>. | ||
== Structure == | == Structure == | ||
| - | In the PDB, this structure is marked as 6OI5 and is noted as the crystal structure of human sulfide quinone oxidoreductase. This enzyme is comprised of two amino acid chains. It contains a ligand, flavin-adenine dinucleotide (FAD). The FAD is noncovalently bound to the main subunit, and it is in the oxidized state<ref name="jackson 1" />. One residue in this structure was modified into <scene name='88/881543/S-mercaptocysteine_-1/1'>s-mercaptocysteine</scene>. This modified residue is considered L-type linking and is a potential drug target . In humans, the SQOR is made of two tandem [ | + | In the PDB, this structure is marked as 6OI5 and is noted as the crystal structure of human sulfide quinone oxidoreductase. This enzyme is comprised of two amino acid chains. It contains a ligand, flavin-adenine dinucleotide (FAD). The FAD is noncovalently bound to the main subunit, and it is in the oxidized state<ref name="jackson 1" />. One residue in this structure was modified into <scene name='88/881543/S-mercaptocysteine_-1/1'>s-mercaptocysteine</scene>. This modified residue is considered L-type linking and is a potential drug target . In humans, the SQOR is made of two tandem [[Rossman_fold]], and a C-terminal made up of two helices. Rossmann folds are composed of six beta sheets that are arranged parallel to one another with alpha helices connecting the first three strands <ref name="jackson 1" />. The C-terminal extends outward from the main body of the enzyme, and is amphipathic, containing both hydrophobic and hydrophilic portions within the enzyme. The <scene name='88/881543/Hydrophobic_regions_-1/1'>hydrophobic region</scene> of the protruding C-terminal faces out from the membrane. Following that C-terminal, a penultimate helix arises and is very hydrophobic. It contains 16 hydrophobic residues, 11 of which are facing away from the membrane. The nonpolar residues on this penultimate helix are most tyrosines and methionines, and they face towards a cavity, indicating a binding location for coenzyme Q <ref name="jackson 1" />. Due to the hydrophobic areas making contact to the inner areas of the membrane, the enzyme would be able to make its way towards coenzyme Q and pass off electrons to it. SQOR contains an indent that is electropositive, which will be the location for sulfane sulfur acceptors to bind. Within the middle of the indent, there is an opening just large enough to give access to the one of the reactive cysteine residues. There is a hydrogen sulfide oxidizing site which connects to a hydrophilic pocket, or tunnel, leading to the location where coenzyme Q will eventually bind <ref name="jackson 1" />. Chain A is composed of alpha helices, beta sheets and has numerous binding sites. Chain A also contains many FAD-binding spots. A disulfide bridge connects the positions 161 to 339, or 201 to 379, also denoted by PDB. The spacing between the two cysteine active sites makes strong bridging between the two. The positions of the disulfide bonds are Cys201 and Cys379. Chain B is very much identical to Chain A in that it contains a <scene name='88/881543/Disulfide_bridge-1/6'>disulfide</scene> bridge at the positions Cys201 and Cys379 <ref name="landry" />. Chain B is also made up of alpha helices and beta sheets. It is very much identical to Chain A in that it has a disulfide bridge at the same residues. The resolution of sulfide quinone oxidoreductase is 2.81 angstroms, and the sequence is 418 residues in length. The surface of SQOR that is facing the membrane is characterized by both positive and negative charges <ref name="jackson 1" />. The surface that is facing towards the cellular matrix contains hydrophobic areas, as well as the hydrophobic coenzyme Q binding pocket. The <scene name='88/881543/Hydrophobic_regions_-1/3'>surface</scene> facing the cellular matrix also has a very large positive charge which interacts with the phospholipid bilayer, which is negative. The other side of SQOR contains a large negative surface, where one of the Rossmann folds is located and where the electropositive divet is located <ref name="jackson 1" />. |
== Function == | == Function == | ||
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== Landmarks on SQOR == | == Landmarks on SQOR == | ||
The FAD binding site on SQOR is a significant landmark in SQOR. FAD is <scene name='88/881543/Fad_-_1/1'>flavin adenine dinucleotide</scene> and is a product of condensation reaction between adenine diphosphate and riboflavin. There are about eleven FAD-binding locations on sulfide quinone oxidoreductase. FAD-binding involves twelve hydrogen bonds to the enzyme, with an addition of interactions with dipoles electrostatically <ref name="jackson 1" />. It is important to note that Lys207 and Lys418 are located near FAD’s binding location, and they are both relatively basic residues. There are also two additional lysine residues at 200 and 344 that are located by the ribityl chain on the FAD <ref name="jackson 1" />. Ribityl chains occur when a terminal hydroxyl group is removed. To help stabilize the charge of the flavin ring, the N-terminus on alpha helix 11 is positioned towards the FAD ring. In addition, alpha helix 1 helps neutralize the charge of the FAD <ref name="jackson 1" />. On the surface of SQOR that is facing the membrane, there is an entrance which leads to the CoQ-binding pocket. Coenzyme Q is very prevalent within cell membranes. This lipid electron transporter, as previously mentioned, is important in SQOR’s pathway to metabolize hydrogen sulfide <ref name="jackson 1" />. Decreased prevalence of coenzyme Q affects the oxidation of hydrogen sulfide, and can cause skin fibroblasts in humans, as recently studied <ref name="quinzii" />. | The FAD binding site on SQOR is a significant landmark in SQOR. FAD is <scene name='88/881543/Fad_-_1/1'>flavin adenine dinucleotide</scene> and is a product of condensation reaction between adenine diphosphate and riboflavin. There are about eleven FAD-binding locations on sulfide quinone oxidoreductase. FAD-binding involves twelve hydrogen bonds to the enzyme, with an addition of interactions with dipoles electrostatically <ref name="jackson 1" />. It is important to note that Lys207 and Lys418 are located near FAD’s binding location, and they are both relatively basic residues. There are also two additional lysine residues at 200 and 344 that are located by the ribityl chain on the FAD <ref name="jackson 1" />. Ribityl chains occur when a terminal hydroxyl group is removed. To help stabilize the charge of the flavin ring, the N-terminus on alpha helix 11 is positioned towards the FAD ring. In addition, alpha helix 1 helps neutralize the charge of the FAD <ref name="jackson 1" />. On the surface of SQOR that is facing the membrane, there is an entrance which leads to the CoQ-binding pocket. Coenzyme Q is very prevalent within cell membranes. This lipid electron transporter, as previously mentioned, is important in SQOR’s pathway to metabolize hydrogen sulfide <ref name="jackson 1" />. Decreased prevalence of coenzyme Q affects the oxidation of hydrogen sulfide, and can cause skin fibroblasts in humans, as recently studied <ref name="quinzii" />. | ||
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| + | ==3D structures of sulfide quinone oxidoreductase== | ||
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| + | [[3D structures of sulfide quinone oxidoreductase]] | ||
| - | This is a sample <scene name='88/881543/Sqor_-_1/1'>scene</scene> created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
| - | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
| + | [[Category:Topic Page]] | ||
Current revision
Contents |
Introduction to SQOR
Oxidoreductases are used to catalyze the movement of electrons between an oxidant and a reductant. Sulfide quinone oxidoreductase or Sulfide:quinone oxidoreductase, , is an integral membrane protein used in the mitochondria during metabolism to oxidize hydrogen sulfide with assistance from a quinone [1]. This enzyme marks the committed step of the sulfide oxidation pathway. SQOR is also the enzyme involved in the irreversible step of hydrogen sulfide metabolism [2]. In the environment, sulfide is found in aquatic marine environments and in soil but is typically produced by prokaryotes and eukaryotes through catabolism [3]. SQOR uses coenzyme Q as the electron acceptor, and it uses sulfide, sulfite, cyanide, or glutathione as a sulfane acceptor [4]. Sulfane, or thiosulfoxide sulfur, is an essential molecule in the regulation of cellular processes. It has the capabilities to create cofactors as well as modify enzymatic activities [5]. Coenzyme Q is essential for electron transfer in metabolic processes, anabolic and catabolic. In bacterial SQOR, cytochrome C is used as the electron acceptor [1]. The gasotransmitter, hydrogen sulfide or H2S, acts in biological processes and can be used as a target in drug interactions, which can be observed in mitochondrial metabolism [1]. Hydrogen sulfide signaling is used in the cardiovascular system to prevent the development of cardiovascular diseases, such as hypertension [1]. SQOR can also be found in bacteria, producing sulfane sulfur metabolites [1]. In contrast to human SQOR, it does not use a sulfane acceptor. In humans, SQOR belongs to the flavoprotein disulfide reductase (FDR) family (Miller, 2013). SQOR is also in the pyridine nucleotide- disulfide oxidoreductase family. There are also various types of SQORs found, such as SqrA, SqrB, SqrC, SqrD, SqrE, and SqrF [3]. The crystallization method used on this SQOR was vapor diffusion at a pH of 7, which in result, gave indicators of the length and structure of this monumental enzyme.
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