Sandbox Reserved 1094: Difference between revisions

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This glucose metabolic process (glycolysis and pentose phosphate pathway) is catalysed by '''G6PD'''. During this process, [[NADH]] is synthesised and used in the heterolactic fermentation and the biosynthesis of fatty acids.

The protein '''G6PD''' also has a role in protecting cells from destruction as it produces the co-factor NADPH which plays a role in protecting cells from reactive oxygen species <ref>PMID: 20608171</ref>.

External resources : glycolysis - click on the Wikipedia description [https://en.wikipedia.org/wiki/Anaerobic_glycolysis] ;

pentose phosphate pathway - click on the Wikipedia description [https://en.wikipedia.org/wiki/Pentose_phosphate_pathway] ;

NADPH - click on the Wikipedia description [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate]

== Genomic context ==

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External resource : click on [https://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1DPG] to see the graphical representation on the RCSB website.

[[Image:Pathology of G6PD deficiency.png|150x150px|upright|thumb| G6PD pathway. Obtained from [https://en.wikipedia.org/wiki/Glucose-6-phosphate_dehydrogenase Wikipedia]]]

== Catalytic activity ==

~~== Catalytic activity ==~~

'''D-glucose 6-phosphate + NAD+ → 6-phospho-D-glucono-1,5-lactone + H+ + NADH'''<ref>PMID: 9485426</ref>

KM=114 µM for '''G6PD''' (with NADP), KM=69 µM for '''G6PD''' (with NAD),

KM=8.0 µM for [[NADP]], KM=160 µM for [[NAD]].

KM=8.0 µM for [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate NADP], KM=160 µM for [[NAD]].

Its regulation depends on the concentration of substrate and coenzyme, rate limiting step in pentose phosphate pathway<ref>PMID: 12033926</ref>.

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== Evolutionary conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

The different structures conserved evolutionary can be observed according to the scale following.

~~[[Image:Consurf_key_small.gif|200px|right]]~~

Check<jmol>

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This sequence being the normal protein sequence found in L. ''mesenteroides''.

== Structural highlights ==

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====''Coenzyme binding domain''====

The coenzyme binding domain binds the [[NAD]] or [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate NADP] which participes in the dehydrogenation of '''G6P'''.

The <scene name='82/829347/Domain_coenzyme2/1'>coenzyme binding domain</scene> binds the [[NAD]] or [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate NADP] which participes in the dehydrogenation of '''G6P'''.

It is defined by a typical [https://scop.berkeley.edu/sunid=30074 β-α-β dinucleotide-binding fold] corresponding to a [https://en.wikipedia.org/wiki/Rossmann_fold Rossman fold].

Only 17 residues over the total of 177 are strictly conserved some of them are involved in turns between some β strands and helices and the three last one of the domain are the first three residues of a strictly conserved nine-residue peptide.

<scene name='82/829347/Arg_46/1'>Arg46</scene> is strictlty conserved and involved in the binding with the 2'-phosphate of NADP. Gln47 could interact both with the 2'-phosphate of NADP or with the 2'-hydroxyl of NAD.

<scene name='82/829347/Arg_46/2'>Arg46</scene> is strictlty conserved and involved in the binding with the 2'-phosphate of NADP. <scene name='82/829347/Gln_47/1'>Gln47</scene> could interact both with the 2'-phosphate of NADP or with the 2'-hydroxyl of NAD.<ref name="struc"/>

====''Carboxyl terminus domain''====

The carboxyl terminus domain is defined by a β+α particular fold which has created his own fold family the [https://scop.berkeley.edu/sunid=39989 G6PD-like]. It is composed of a large essentially antiparallel curved nine-stranded β-sheet with 11 helices and remain well ordered to the carboxy-terminal residue. It is essential in the activity of the enzyme because it ensure the formation of the tertiary and the quaternary structure.

The <scene name='82/829347/Domain_cter2/1'>carboxyl terminus domain</scene> is defined by a β+α particular fold which has created his own fold family the [https://scop.berkeley.edu/sunid=39989 G6PD-like]. It is composed of a large essentially antiparallel curved nine-stranded β-sheet with 11 helices and remain well ordered to the carboxy-terminal residue. It is essential in the activity of the enzyme because it ensure the formation of the [https://en.wikipedia.org/wiki/Protein_tertiary_structure tertiary] and the [https://en.wikipedia.org/wiki/Protein_quaternary_structure quaternary] structure.<ref name="struc"/>

====''Domain boundary''====

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At the boundary between the two domains some helices of the carboxy terminus domain interacts with multiples β strands and helices of the coenzyme binding domain ensuring the cohesion of the enzyme monomer.

There is a pocket where the phosphate of the substrate binds. Residues involved in the contact with the phosphate are His178, Glu147, Lys 148, Tyr 415 and Ile176.

There is a <scene name='82/829347/Pocket/1'>pocket</scene> where the phosphate of the substrate binds. Residues involved in the contact with the phosphate are His178, Glu147, Lys 148, Tyr 415 and Ile176.

Asp177 and His240 are two basic residues conserved and localized in the binding pocket which could act as base for the deshydrogenation reaction. Site-directed mutagenesis has shown that H240N mutant have a lower activity than the wild-type enzyme. So it has been deduced that His240 is involved as the base of the reaction.

Asp177 and His240 are two basic residues conserved and localized in the binding pocket which could act as base for the deshydrogenation reaction. [https://en.wikipedia.org/wiki/Site-directed_mutagenesis Site-directed mutagenesis] has shown that H240N mutant have a lower activity than the wild-type enzyme. So it has been deduced that <scene name='82/829347/His240/1'>His240</scene> is involved as the base of the reaction.<ref name="struc"/>

==='''Quaternary structure'''===

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The dimer is very extend compared to the monomer with a size of 112Å.

The enzyme is found into a dimeric form in vivo. The two subunits interface is made by the contact between the two antiparallels β-sheets of the carboxyl terminus domain. Their interaction is crucial and form a β-half-barrel ([https://en.wikipedia.org/wiki/Beta_barrel β-Barrel ]) on one side of the protein which is closed on the other side by helices of each monomer. The majority of dimer contacts are hydrophobic with hydrophobic residues in the inside of the β-half-barrel but there are three salt bridges, especially a conserved one between Glu183 and Lys386 ; Lys 32 with Asp 390 and Arg395 with Asp 407, and two main chain hydrogen bonds which participates to the cohesion of the structure. Glu183 is the last residue of the nine-residue conserved peptide.

The enzyme is found into a dimeric form in vivo. The two subunits interface is made by the contact between the two antiparallels β-sheets of the carboxyl terminus domain. Their interaction is crucial and form a <scene name='82/829347/Betahalfbarrel/1'>β-half-barrel</scene> ([https://en.wikipedia.org/wiki/Beta_barrel β-Barrel ]) on one side of the protein which is closed on the other side by helices of each monomer. The majority of dimer contacts are hydrophobic with hydrophobic residues in the inside of the β-half-barrel but there are <scene name='82/829347/Saltbridges/1'>three salt bridges</scene>, especially a conserved one between Glu183 and Lys386 ; Lys 32 with Asp 390 and Arg395 with Asp 407, and two main chain hydrogen bonds which participates to the cohesion of the structure. Glu183 is the last residue of the nine-residue conserved peptide.<ref name="struc"/>

The active site of the enzyme is contained in each monomer but the dimeric form is necessary to the biological activity indeed it confers the stability in aqueous medium.

Sandbox Reserved 1094: Difference between revisions

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@@ Line 9: / Line 9: @@
 This glucose metabolic process (glycolysis and pentose phosphate pathway) is catalysed by '''G6PD'''. During this process, [[NADH]] is synthesised and used in the heterolactic fermentation and the biosynthesis of fatty acids.
 The protein '''G6PD''' also has a role in protecting cells from destruction as it produces the co-factor NADPH which plays a role in protecting cells from reactive oxygen species <ref>PMID: 20608171</ref>.
+<font color='grey'>External resources</font> : glycolysis - click on the Wikipedia description [https://en.wikipedia.org/wiki/Anaerobic_glycolysis] ;
+pentose phosphate pathway - click on the Wikipedia description [https://en.wikipedia.org/wiki/Pentose_phosphate_pathway] ;
+NADPH - click on the Wikipedia description [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate]
 == Genomic context ==
@@ Line 15: / Line 19: @@
 <font color='grey'>External resource</font> : click on [https://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1DPG] to see the graphical representation on the RCSB website.
+[[Image:Pathology of G6PD deficiency.png|150x150px|upright|thumb| G6PD pathway. Obtained from [https://en.wikipedia.org/wiki/Glucose-6-phosphate_dehydrogenase Wikipedia]]]
+== Catalytic activity ==
-== Catalytic activity ==
 <font color='red'>'''D-glucose 6-phosphate + NAD+ → 6-phospho-D-glucono-1,5-lactone + H+ + NADH'''<ref>PMID: 9485426</ref></font>
 KM=114 µM for '''G6PD''' (with NADP), KM=69 µM for '''G6PD''' (with NAD),
-KM=8.0 µM for [[NADP]], KM=160 µM for [[NAD]].
+KM=8.0 µM for [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate NADP], KM=160 µM for [[NAD]].
 Its regulation depends on the concentration of substrate and coenzyme, rate limiting step in pentose phosphate pathway<ref>PMID: 12033926</ref>.
@@ Line 28: / Line 34: @@
 == Evolutionary conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
 The different structures conserved evolutionary can be observed according to the scale following.
-[[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
@@ Line 48: / Line 55: @@
 This sequence being the normal protein sequence found in L. ''mesenteroides''.
-<Structure load='1dpg' size='450' frame='true' align='right' caption='Insert caption here' scene='' />
+<Structure load='1dpg' size='450' frame='true' align='right' caption='3D structure of G6PD' scene='' />
 == Structural highlights ==
@@ Line 64: / Line 71: @@
 ====''Coenzyme binding domain''====
-The coenzyme binding domain binds the [[NAD]] or [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate NADP]  which participes in the dehydrogenation of '''G6P'''.
+The <scene name='82/829347/Domain_coenzyme2/1'>coenzyme binding domain</scene> binds the [[NAD]] or [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate NADP]  which participes in the dehydrogenation of '''G6P'''.
 It is defined by a typical [https://scop.berkeley.edu/sunid=30074 β-α-β dinucleotide-binding fold] corresponding to a [https://en.wikipedia.org/wiki/Rossmann_fold Rossman fold].
 Only 17 residues over the total of 177 are strictly conserved some of them are involved in turns between some β strands and helices and the three last one of the domain are the first three residues of a strictly conserved nine-residue peptide.
-<scene name='82/829347/Arg_46/1'>Arg46</scene> is strictlty conserved and involved in the binding with the 2'-phosphate of NADP. Gln47 could interact both with the 2'-phosphate of NADP or with the 2'-hydroxyl of NAD.
+<scene name='82/829347/Arg_46/2'>Arg46</scene> is strictlty conserved and involved in the binding with the 2'-phosphate of NADP. <scene name='82/829347/Gln_47/1'>Gln47</scene> could interact both with the 2'-phosphate of NADP or with the 2'-hydroxyl of NAD.<ref name="struc"/>
 ====''Carboxyl terminus domain''====
-The carboxyl terminus domain is defined by a β+α particular fold which has created his own fold family the [https://scop.berkeley.edu/sunid=39989 G6PD-like]. It is composed of a large essentially antiparallel curved nine-stranded β-sheet with 11 helices and remain well ordered to the carboxy-terminal residue. It is essential in the activity of the enzyme because it ensure the formation of the tertiary and the quaternary structure.
+The <scene name='82/829347/Domain_cter2/1'>carboxyl terminus domain</scene> is defined by a β+α particular fold which has created his own fold family the [https://scop.berkeley.edu/sunid=39989 G6PD-like]. It is composed of a large essentially antiparallel curved nine-stranded β-sheet with 11 helices and remain well ordered to the carboxy-terminal residue. It is essential in the activity of the enzyme because it ensure the formation of the [https://en.wikipedia.org/wiki/Protein_tertiary_structure tertiary] and the [https://en.wikipedia.org/wiki/Protein_quaternary_structure quaternary] structure.<ref name="struc"/>
 ====''Domain boundary''====
@@ Line 77: / Line 84: @@
 At the boundary between the two domains some helices of the carboxy terminus domain interacts with multiples β strands and helices of the coenzyme binding domain ensuring the cohesion of the enzyme monomer.
-There is a pocket where the phosphate of the substrate binds. Residues involved in the contact with the phosphate are His178, Glu147, Lys 148, Tyr 415 and Ile176.
+There is a <scene name='82/829347/Pocket/1'>pocket</scene> where the phosphate of the substrate binds. Residues involved in the contact with the phosphate are His178, Glu147, Lys 148, Tyr 415 and Ile176.
-Asp177 and His240 are two basic residues conserved and localized in the binding pocket which could act as base for the deshydrogenation reaction. Site-directed mutagenesis has shown that H240N mutant have a lower activity than the wild-type enzyme. So it has been deduced that His240 is involved as the base of the reaction.
+Asp177 and His240 are two basic residues conserved and localized in the binding pocket which could act as base for the deshydrogenation reaction. [https://en.wikipedia.org/wiki/Site-directed_mutagenesis Site-directed mutagenesis] has shown that H240N mutant have a lower activity than the wild-type enzyme. So it has been deduced that <scene name='82/829347/His240/1'>His240</scene> is involved as the base of the reaction.<ref name="struc"/>
 ==='''Quaternary structure'''===
@@ Line 87: / Line 94: @@
 The dimer is very extend compared to the monomer with a size of 112Å.
-The enzyme is found into a dimeric form in vivo. The two subunits interface is made by the contact between the two antiparallels β-sheets of the carboxyl terminus domain. Their interaction is crucial and form a β-half-barrel ([https://en.wikipedia.org/wiki/Beta_barrel β-Barrel ]) on one side of the protein which is closed on the other side by helices of each monomer. The majority of dimer contacts are hydrophobic with hydrophobic residues in the inside of the β-half-barrel but there are three salt bridges, especially a conserved one between Glu183 and Lys386 ; Lys 32 with Asp 390 and Arg395 with Asp 407, and two main chain hydrogen bonds which participates to the cohesion of the structure. Glu183 is the last residue of the nine-residue conserved peptide.
+The enzyme is found into a dimeric form in vivo. The two subunits interface is made by the contact between the two antiparallels β-sheets of the carboxyl terminus domain. Their interaction is crucial and form a <scene name='82/829347/Betahalfbarrel/1'>β-half-barrel</scene> ([https://en.wikipedia.org/wiki/Beta_barrel β-Barrel ]) on one side of the protein which is closed on the other side by helices of each monomer. The majority of dimer contacts are hydrophobic with hydrophobic residues in the inside of the β-half-barrel but there are <scene name='82/829347/Saltbridges/1'>three salt bridges</scene>, especially a conserved one between Glu183 and Lys386 ; Lys 32 with Asp 390 and Arg395 with Asp 407, and two main chain hydrogen bonds which participates to the cohesion of the structure. Glu183 is the last residue of the nine-residue conserved peptide.<ref name="struc"/>
 The active site of the enzyme is contained in each monomer but the dimeric form is necessary to the biological activity indeed it confers the stability in aqueous medium.