Sandbox Reserved 1094: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| (46 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
{{Sandbox_ESBS_2019}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | {{Sandbox_ESBS_2019}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
==Glucose-6-Phosphate Dehydrogenase from Leuconostoc ''mesenteroides''== | ==Glucose-6-Phosphate Dehydrogenase from Leuconostoc ''mesenteroides''== | ||
The protein''' Glucose-6-Phosphate Dehydrogenase''' is an enzyme involved in the metabolic pathways of the majority of organisms. Leuconostoc ''mesenteroides'' is a Bacilli <font color='purple'>Gram-positive</font> bacterium that expresses this enzyme. | |||
== Function == | == Function == | ||
G6PD plays an important role in the metabolism of L.''mesenteroides''. | '''G6PD''' plays an important role in the metabolism of L.''mesenteroides''. | ||
L.''mesenteroides'' is a facultactively anaerobic micro-organism which metabolizes glucose to generate lactic acid, ethanol but also carbon dioxyde. | |||
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. | 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>. | 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 == | == Genomic context == | ||
It is coded by the G6PD gene (1461 nucleotides)<ref>GeneID:29577449</ref>. | It is coded by the '''G6PD''' gene (1461 nucleotides)<ref>GeneID:29577449</ref>. | ||
It has in total 2 chains. In the link below, these two chains are represented by one unique sequence entity. | It has in total 2 chains. In the link below, these two chains are represented by one unique sequence entity. | ||
<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 == | ||
KM=114 µM for G6PD (with NADP), KM=69 µM for G6PD (with NAD), | <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>. | Its regulation depends on the concentration of substrate and coenzyme, rate limiting step in pentose phosphate pathway<ref>PMID: 12033926</ref>. | ||
| Line 27: | Line 34: | ||
== Evolutionary conservation == | == Evolutionary conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | |||
The different structures conserved evolutionary can be observed according to the scale following. | The different structures conserved evolutionary can be observed according to the scale following. | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| Line 44: | Line 52: | ||
The most common mutations in the amino acids sequence found that induce a loss of catalytic activity are a substitution of the bold amino acids by another one<ref>PMID: 11106479</ref>: | The most common mutations in the amino acids sequence found that induce a loss of catalytic activity are a substitution of the bold amino acids by another one<ref>PMID: 11106479</ref>: | ||
MVSEIKTLVT FFGG '''T''' GDLAK R ''' | MVSEIKTLVT FFGG <font color='turquoise'>'''T'''</font> GDLAK R <font color='turquoise'>'''TK'''</font> LYPSVFNL YKKGYLQKHF AIVGTA <font color='turquoise'>'''RQ'''</font> AL NDDEFKQLVR DSIKDFTDDQ AQAEAFIEHF SYRAHDVTDA ASYAVLKEAI EEAADKFDID GNRIFYMSVA PRFFGTIAKY LKSEGLLADT GYNRLMIEK <font color='turquoise'>'''P'''</font> FGTSYDTAAE LQNDLENAFD DNQLFRI <font color='turquoise'>'''DHY'''</font> LG <font color='turquoise'>'''K'''</font> EMVQNIA ALRFGNPIFD AAWNKDYIKN VQVTLSEVLG VEERAGYYDT AGALLDMIQN <font color='turquoise'>'''H''' </font> TMQIVGWLA MEKPESFTDK DIRAAKNAAF NALKIYDEAE VNKYFVRAQY GAGDSADFKP YLEELDVPAD SKNNTFIAGE LQFDLPRWEG VPFYVRSGKR LAA <font color='turquoise'> '''K''' </font> QTRVDI VFKAGTFNFG SEQEAQEAVL SIII <font color='turquoise'> '''D''' </font> PKGAI ELKLNAKSVE DAFNTRTIDL GWTVSDEDKK NTPEP <font color='turquoise'> '''Y''' </font> ERMI HDTMNGDGSN FADWNGVSIA WKFVDAISAV YTADKAPLET YKSGSMGPEA SDKLLAANGD AWVFKG. | ||
This sequence being the normal protein sequence found in L. ''mesenteroides''. | This sequence being the normal protein sequence found in L. ''mesenteroides''. | ||
<Structure load='1dpg' size='450' frame='true' align='right' caption='3D structure of G6PD' scene='' /> | |||
== Structural highlights == | |||
Glucose-6-Phosphate Dehydrogenase is formed of a homodimer, so a dimer of two identical [https://en.wikipedia.org/wiki/Protein_subunit subunit]. | |||
==='''Secondary structure'''=== | |||
A subunit contains 485 residues where 285 residues are in secondary structure. 93 residues are involved in 15 β-sheet strands and 192 in 17 helices respectively represented in <scene name='82/829347/Brin_beta_et_helices_monomer/1'>red and green</scene>.<ref name="struc">PMID: 7881907</ref> | |||
==='''Tertiary structure'''=== | |||
Each <scene name='82/829347/Monomerg6pd/2'>monomer</scene> is composed of 2 domains. A small domain localized in the amino terminal part (<scene name='82/829347/Domain_coenzyme/1'>residues 1-177</scene>) which constitute the coenzyme binding domain and a larger domain in the carboxyl terminal part (<scene name='82/829347/Domain_cter/1'>residues 178-485</scene>).<ref name="struc"/> | |||
====''Coenzyme binding domain''==== | |||
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_46/2'>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 <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''==== | |||
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 <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. [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'''=== | |||
''Dimer'' | |||
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 <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. | |||
== References == | == References == | ||
<references/> | <references/> | ||
