Auxiliary Activity Family 13 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:16:18Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Harry Brumer at 17:34, 4 November 2019

2019-11-04T17:34:50Z

Gideon Davies at 10:58, 22 February 2019

2019-02-22T10:58:00Z

Glyn Hemsworth at 09:33, 19 February 2019

2019-02-19T09:33:19Z

Glyn Hemsworth at 09:57, 18 February 2019

2019-02-18T09:57:55Z

Glyn Hemsworth at 09:54, 18 February 2019

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Glyn Hemsworth at 09:50, 18 February 2019

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Glyn Hemsworth at 13:50, 14 February 2019

2019-02-14T13:50:58Z

Glyn Hemsworth at 13:49, 14 February 2019

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Glyn Hemsworth at 13:32, 14 February 2019

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Glyn Hemsworth^^^ & ^^^Leila LoLeggio^^^
+* [[Author]]: [[User:Glyn Hemsworth|Glyn Hemsworth]] & [[User:Leila LoLeggio|Leila LoLeggio]]
-* [[Responsible Curator]]:  ^^^Gideon Davies^^^
+* [[Responsible Curator]]:  [[User:Gideon Davies|Gideon Davies]]
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← Older revision		Revision as of 17:34, 4 November 2019
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	</biblio>		</biblio>

−	[[Category:Auxiliary Activity Families\|~~AA13~~]]	+	[[Category:Auxiliary Activity Families\|AA013]]

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: ^^^Glyn Hemsworth^^^ & ^^^Leila LoLeggio^^^
 * [[Responsible Curator]]:  ^^^Gideon Davies^^^
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 == Substrate specificities ==
-The AA13 family represents the fourth family of Lytic Polysaccharide Monooxygenases (LPMOs) that has been identified. Found in fungi, the first member of this family to be identified and characterised in the academic literature was isolated from <i>Neurospora crassa</i> by Vu et al <cite>Vu2014</cite>. While searching the <i>Neurospora crassa</i> genome for new putative LPMO sequences, they identified a sequence that appeared to code for an LPMO with a C-terminal [[CBM20]] domain but lacked significant overall sequence similarity to other [[AA9]], [[AA10]] or [[AA11]] LPMOs. Not long after Lo Leggio et al <cite>LoLeggio2015</cite> also identified and characterised AA13 family members from <i>Aspergilllus nidulans</i> and <i>Aspergillus oryzae</i> using a similar approach. Prior to this, genes now known to code for AA13s were demonstrated to produce proteins capable of boosting &alpha; and &beta;-amylase activity during starch, amylose and amylopectin degradation ([{{PatentLink}}WO2014197705A1 WO2014197705A1]).
+The AA13 family represents the fourth family of (Lytic) Polysaccharide Monooxygenases (LPMOs / sometimes called PMOs) that has been identified. Found in fungi, the first member of this family to be identified and characterised in the academic literature was isolated from <i>Neurospora crassa</i> by Vu et al <cite>Vu2014</cite>. While searching the <i>Neurospora crassa</i> genome for new putative LPMO sequences, they identified a sequence that appeared to code for an LPMO with a C-terminal [[CBM20]] domain but lacked significant overall sequence similarity to other [[AA9]], [[AA10]] or [[AA11]] LPMOs. Subsequently, Lo Leggio et al <cite>LoLeggio2015</cite> also identified and characterised AA13 family members from <i>Aspergilllus nidulans</i> and <i>Aspergillus oryzae</i> using a similar approach. Prior to this, genes now known to code for AA13s were demonstrated to produce proteins capable of boosting &alpha; and &beta;-amylase activity during starch, amylose and amylopectin degradation ([{{PatentLink}}WO2014197705A1 WO2014197705A1]).
 Of the AA13s that have been biochemically characterised to date, activity has only been demonstrate on starch and related substrates <cite>Vu2014 LoLeggio2015</cite>. The expression of these enzymes has also been shown to be heavily unregulated during growth of  <i>A. nidulans</i> on starch <cite>Nekiunaite2016a</cite>. As for other LPMOs, AA13s utilise copper and an electron donor to oxidatively introduce chain breaks into the &alpha;-1,4-linked glucose polymers that form starch <cite>Vu2014 LoLeggio2015</cite>. AA13s specifically attack at the C1 position of the sugar ring forming oligosaccharide products with lactones at the reducing end which are then additionally hydrated to form aldonic acid terminated maltodextrins <cite>LoLeggio2015</cite>. The C1 specificity suggests that these LPMOs should be able to oxidatively attack both the &alpha;-1,4- and &alpha;-1,6-linkages found in amylopectin <cite>Vu2015</cite>. Interestingly, AA13s are currently the only LPMOs characterised to date that act on a glucan polymer formed from anything other than &beta;-1,4-linkages <cite>Vu2016</cite>.

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 == Catalytic Residues ==
-The “histidine brace” motif is used to bind the active site copper in AA13 <cite>LoLeggio2015</cite>, as it is for all other LPMOs studied to date ([[AA9]], [[AA10]] & [[AA11]]) <cite>Vaaje-Kolstad2017</cite>. This motif sees the amino group and imidazole side chain of the N-terminal histidine, together with the imidazole group of a second histidine, directly coordinate the copper ion in a T-shaped geometry. For AA13s, one axial position is occupied by a tyrosine on one side of the copper ion, with a loop containing a glycine approaching near to the copper on the other side (Figure 2, top) <cite>LoLeggio2015</cite>. In [[AA10]]s and [[AA11]]s alanine in this position has been suggested as a possible important factor in distorting the arrangement of water molecules around the active site which may have mechanistic consequences in these families <cite>Hemworth2013 Hemsworth2014</cite>. An interesting feature of the electron paramagnetic resonance (EPR) spectrum observed for the <i>A. nidulans</i> and <i>A. oryzae</i> AA13s was the presence of superhyperfine coupling in the spectrum (Figure 2, bottom) <cite>LoLeggio2015</cite>.
+The “histidine brace” motif is used to bind the active site copper in AA13 <cite>LoLeggio2015</cite>, as it is for all other LPMOs studied to date ([[AA9]], [[AA10]] & [[AA11]]) <cite>Vaaje-Kolstad2017</cite>. This motif sees the amino group and imidazole side chain of the N-terminal histidine, together with the imidazole group of a second histidine, directly coordinate the copper ion in a T-shaped geometry. For AA13s, one axial position is occupied by a tyrosine on one side of the copper ion, with a loop containing a glycine approaching near to the copper on the other side (Figure 2, top) <cite>LoLeggio2015</cite>. In [[AA10]]s and [[AA11]]s alanine in this position has been suggested as a possible important factor in distorting the arrangement of water molecules around the active site which may have mechanistic consequences in these families <cite>Hemsworth2013 Hemsworth2014</cite>. An interesting feature of the electron paramagnetic resonance (EPR) spectrum observed for the <i>A. nidulans</i> and <i>A. oryzae</i> AA13s was the presence of superhyperfine coupling in the spectrum (Figure 2, bottom) <cite>LoLeggio2015</cite>.
 == Family Firsts ==

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 #Frandsen2017 pmid=28045386
 </biblio>
 [[Category:Auxiliary Activity Families|AA13]]

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 #Vu2016 pmid=27170366
 #Walton2017 pmid=27094791
 #Nekiunaite2017b pmid=27397613
 #Vaaje-Kolstad2017 pmid=28086105
 #Frandsen2017 pmid=28045386
 </biblio>
 [[Category:Auxiliary Activity Families|AA13]]

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 <!-- The data in the table below should be updated by the Author/Curator according to current information on the family -->
 <div style="float:right">
 {| {{Prettytable}}
 |-
 |{{Hl2}} colspan="2" align="center" |'''Auxiliary Activity Family 13'''
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 All LPMOs ([[AA9]], [[AA10]], [[AA11]], & AA13) are copper dependent monooxygenases and there is considerable work ongoing in trying to elucidate their detailed reaction mechanism <cite>Walton2017</cite>. Starch, being an &alpha;-1,4-linked substrate, poses a different challenge for AA13s to be able to oxidatively attack at the C1 carbon. Whether there is a significant difference in mechanism required in order to oxidise starch is currently unclear.
 Performing kinetic measurements on LPMOs has been notoriously difficult. Several key aspects of AA13 biochemistry have been observed however. The <i>A. nidulans</i> AA13 showed significant synergy with a &beta;-amylase during degradation assays using retrograded starch as the substrate. The combined action of these enzymes resulted in >100-fold increase in the release of maltose compared to &beta;-amylase acting alone, representing one of the most significant boosting activities observed so far for any LPMO <cite>LoLeggio2015</cite>. Also highlighted in this study was the importance of the reducing agent used to activate the enzyme with cysteine providing greater activity than ascorbate which is typically used to activate LPMOs. Vu et al <cite>Vu2014</cite> also showed that cellobiose dehydrogenase (CDH composed of [[AA3]] and [[AA8]] domains) represents a good activating partner for AA13s as has been observed for [[AA9]]s. The importance of the [[CBM20]] module for AA13 activity has also been highlighted. The <i>A. oryzae</i> AA13, which naturally lacks a CBM, did not appear to be active in assays on starch while the [[CBM20]] appended A.nidulans enzyme showed clear activity <cite>LoLeggio2015</cite>. Indeed the presence of the [[CBM20]] domain has been demonstrated to confer typical starch and &beta;-cyclodextrin binding properties to AA13s and is suggested to mediate most of the substrate binding properties of this family of enzymes <cite>Nekiunaite2017b</cite>.
 == Three-dimensional structures ==
 The core fold of the AA13 structure is similar to all other LPMOs ([[AA9]], [[AA10]], & [[AA11]]) representing a &beta;-sandwich immunoglobulin like fold <cite>LoLeggio2015</cite>. There are some significant structural differences compared to the other families however. Firstly, the AA13 structure reveals additional helical secondary structure elements that are not found in other LPMOs (Figure 1). The most prominent difference however is surrounding the copper active site. Where in other LPMOs, the copper histidine brace is found at the centre of a flat or slightly concave surface ([[AA9]], [[AA10]], & [[AA11]]), a distinct groove can be observed passing over the active site of AA13 (Figure 1). This is an adaptation that is thought to be necessary to accommodate the helical structure of an amylopectin substrate. Despite significant efforts, it has not been possible to determine an oligosaccharide bound structure for an AA13 which would be particularly beneficial to delineating the adaptions necessary to allow activity on an &alpha;-1,4-linked substrate <cite>Frandsen2017</cite>.
 == Catalytic Residues ==