Syn/anti lateral protonation

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• Author: ^^^Wim Nerinckx^^^
• Responsible Curator: ^^^Spencer Williams^^^

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Overview

This page provides a table that summarizes the spatial positioning of the catalytic general acid residue in the active sites of glycoside hydrolases, relative to the substrate. The table below updates those found in the seminal paper on this concept by Heightman and Vasella [1], and a following paper by Nerinckx et al. [2].

Background

The "not from above, but from the side" concept of semi-lateral glycosidic oxygen protonation by glycoside hydrolases was introduced by Heightman and Vasella [1]. It was originally only described for beta-equatorial glycoside hydrolases, but appears to be equally applicable to enzymes acting on an alpha-axial glycosidic bond [2]. When dividing subsite -1 into half-spaces by a plane defined by the glycosidic oxygen and C1' and H1' of the –1 glycoside, many ligand-complexed structures reveal that the proton donor is positioned either in the syn half-space (near the ring-oxygen of the –1 glycoside), or in the anti half-space (on the opposite side of the ring-oxygen). Members of the same GH family appear to share a common syn or anti protonator arrangement and further, this specificity appears to be preserved within Clans of families. This page's compilation of subsite -1 occupied complexes shows that about 70% of all GH families are anti protonators.

Closer inspection of crystal structures of –1/+1 subsite-spanning substrates, or substrate-analogue ligands, in complex with enzymes reveals a further intriguing corollary [2, 3]. In substrate-bound complexes with anti protonating GH enzymes, the scissile anomeric bond (often studied using the thio-analogue) shows a dihedral angle φ (O5'-C1'-[O,S]x-Cx) that is in the lowest-energy synclinal (gauche) conformation. The rationale for this is that a minus synclinal dihedral angle φ for an equatorial glycosidic bond, or plus synclinal for an axial glycosidic bond [4], allows for hyperconjugative overlap of the C1'-O5' antibonding orbital with an antiperiplanar-oriented lone pair orbital lobe of the glycosidic oxygen, thereby creating partial double bond character and stabilization of the glycosidic bond by 4–5 kcal/mol; this ground-state stabilizing phenomenon is known as the ‘exo-anomeric effect’ [5, 6, 7]. Anti protonation occurs on the glycosidic oxygen’s antiperiplanar lone pair, thereby removing the stabilizing exo-anomeric effect. This suggests that anti protonation is an enzymic approach for lowering the activation barrier leading to the transition state (Figure 1 centre).

Syn protonating glycoside hydrolases apparently make use of a different approach [2, 3]. In many –1/+1 subsite-spanning ligand complexes, the dihedral angle φ of the scissile anomeric bond has been rotated away from its lowest-energy synclinal position: clockwise to minus-anticlinal or antiperiplanar for beta-equatorial; counterclockwise to plus-anticlinal or antiperiplanar for alpha-axial anomeric bonds. This removes the hyperconjugative overlap and thus also the stabilizing exo-anomeric effect. And because of this rotation, a lone pair of the glycosidic oxygen is directed into the syn half-space, allowing it to be protonated by the syn-positioned proton donor (Figure 1 right).

Figure 1. Newman projections, with the glycosidic oxygen as proximal atom and the anomeric carbon as distal atom, showing anti (centre) versus syn (right) semi-lateral protonation in beta-equatorial (top) and alpha-axial (bottom) glycoside hydrolases. The indicated φ is the dihedral angle for O5'-C1'-O4-C4.

Table of syn/anti protonation examples

This table contains only one example per GH family of a ligand-complexed protein structure where the syn or anti positioning of the proton donor can be clearly observed; other examples may be available on a family-by-family basis. The reader is thus advised to consult the CAZy database for a current, comprehensive list of CAZyme structures. Where available, the selected examples are Michaelis-type complexes with the ligand spanning the -1/+1 subsites, since these have an intact glycosidic or thioglycosidic bond, or are N-analogs of the substrate (e.g. acarbose). In some examples, the proton donor has been mutated (e.g., to the corresponding amide or to an alanine), and in those cases one may wish to look at a superposition of the given PDB example with the structure of the native enzyme. If a Michaelis-type complex is not yet available, the second and third example choices, respectively, are trapped glycosyl-enzyme intermediates and product complexes where subsite -1 is occupied.

Please also be aware that this is a large table with many data. Please contact the page Author or Responsible Curator with corrections.

Table

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Family	Clan	Structure fold	Anomeric specificity	Mechanism	Syn/anti protonator	Example PDB ID	Enzyme	Organism	Ligand	General acid	Nucleophile or General base	Reference
GH1	A	(β/α)8	beta-d	retaining	anti	2cer	β-glycosidase S	Sulfolobus solfataricus P2	phenethyl glucoimidazole	Glu206	Glu387	[8]
GH2	A	(β/α)8	beta-d / alpha-l	retaining	anti	2vzu	exo-β-glucosaminidase	Amicolatopsis orientalis	PNP-β-d-glucosamine	Glu469	Glu541	[9]
GH3	none	(β/α)8	beta-d / alpha-l	retaining	anti	1iex	exo-1,3-1,4-glucanase	Hordeum vulgare	thiocellobiose	Glu491	Asp285	[10]
GH5	A	(β/α)8	beta-d	retaining	anti	1h2j	endo-β-1,4-glucanase	Bacillus agaradhaerens	2',4'-DNP-2-F-cellobioside	Glu129	Glu228	[11]
GH6	none	(β/α)8	beta-d	inverting	syn	1qjw	cellobiohydrolase 2	Hypocrea jecorina	(Glc)2-S-(Glc)2	Asp221	debated	[12]
GH7	B	β-jelly roll	beta-d	retaining	syn	1ovw	endo-1,4-glucanase	Fusarium oxysporum	thio-(Glc)5	Glu202	Glu197	[13]
GH8	M	(α/α)6	beta-d	inverting	anti	1kwf	endo-1,4-glucanase	Clostridium thermocellum	cellopentaose	Glu95	Asp278	[14]
GH9	none	(α/α)6	beta-d	inverting	syn	1rq5	cellobiohydrolase	Clostridium thermocellum	cellotetraose	Glu795	Asp383	[15]
GH10	A	(β/α)8	beta-d	retaining	anti	2d24	β-1,4-xylanase	Streptomyces olivaceoviridis E-86	xylopentaose	Glu128	Glu236	[16]
GH11	C	β-jelly roll	beta-d	retaining	syn	4hk8	endo-β-1,4-xylanase	Hypocrea jecorina	xylohexaose	Glu177	Glu86	[17]
GH12	C	β-jelly roll	beta-d	retaining	syn	1w2u	endoglucanase	Humicola grisea	thiocellotetraose	Glu205	Glu120	[18]
GH13	H	(β/α)8	alpha-d	retaining	anti	1cxk	β-cyclodextrin glucanotransferase	Bacillus circulans	maltononaose	Glu257	Asp229	[19]
GH14	none	(β/α)8	alpha-d	inverting	syn	1itc	β-amylase	Bacillus cereus	maltopentaose	Glu172	Glu367	[20]
GH15	L	(α/α)6	alpha-d	inverting	anti	1dog	glucoamylase	Aspergillus awamori	1-deoxynojirimycin	Glu179	Glu400	[21]
GH16	B	β-jelly roll	beta-d	retaining	syn	1urx	β-agarase A	Zobellia galactanivorans	oligoagarose	Glu152	Glu147	[22]
GH17	A	(β/α)8	beta-d	retaining	anti	4gzj	endo-β-1,3-glucanase	Solanum tuberosum	laminaratriose + laminarabiose	Glu118	Glu259	[23]
GH18	K	(β/α)8	beta-d	retaining	anti	1ffr	chitinase A	Serratia marcescens	(NAG)6	Glu315	internal	[24]
GH19	none	lysozyme type	beta-d	inverting	syn	3wh1	chitinase	Bryum coronatum	(GlcNAc)4	Glu61	Glu70	[25]
GH20	K	(β/α)8	beta-d	retaining	anti	1c7s	chitobiase	Serratia marcescens	chitobiose	Glu540	internal	[26]
GH22	none	lysozyme type	beta-d	retaining	syn	1h6m	lysozyme C	Gallus gallus	Chit-2-F-chitosyl	Glu35	Asp52	[27]
GH23	none	lysozyme type	beta-d	inverting	syn	1lsp	lysozyme G	Cygnus atratus	Bulgecin A	Glu73	internal	[28]
GH24	I	α + β	beta-d	inverting	syn	148l	lysozyme E	Bacteriophage T4	chitobiosyl	Glu11	Glu26	[29]
GH26	A	(β/α)8	beta-d	retaining	anti	2vx6	exo-β-mannanase	Cellvibrio japonicus Ueda107	Gal1Man4	Glu221	Glu338	[30]
GH27	D	(β/α)8	alpha-d / beta-l	retaining	anti	3lrm	α-galactosidase	Saccharomyces cerevisiae	raffinose	Asp209	Asp141	[31]
GH28	N	β-helix	alpha-d (and α-l-rham)	inverting	anti	2uvf	exo-polygalacturonosidase	Yersinia enterocolitica ATCC9610D	digalacturonic acid	Asp402	Asp381 Asp403	[32]
GH29	R	(β/α)8	alpha-l	retaining	syn	3uet	α-1,3/4-fucosidase	Bifidobacterium longum subsp. infantis	lacto-N-fucopentaose II	Glu217	Asp172	[33]
GH30	A	(β/α)8	beta-d	retaining	anti	2y24	glucurono-xylanase	Dickea chrysanthemi D1	glucuronoxylan tetrasaccharide	Glu163	Glu253	[34]
GH31	D	(β/α)8	alpha-d	retaining	anti	2qmj	maltase-glucoamylase	Homo sapiens	acarbose	Asp542	Asp443	[35]
GH32	J	5-fold β-propeller	beta-d	retaining	anti	2add	fructan β-(2,1)-fructosidase	Cichorium intybus	sucrose	Glu201	Asp22	[36]
GH33	E	6-fold β-propeller	alpha-d	retaining	anti	1s0i	transsialidase	Trypanosoma cruzi	sialyllactose	Asp59	Tyr342	[37]
GH34	E	6-fold β-propeller	alpha-d	retaining	anti	4gzw	N2 neuraminidase	Influenza A Tanzania/205/2010 H3N2	α-d-Neup5Ac-(2,3)-β-d-Galp-(1,4)-β-d-GlcpNAc	Asp151	Tyr406	[38]
GH35	A	(β/α)8	beta-d	retaining	anti	3ogv	β-galactosidase	Hypocrea jecorina	2-phenylethyl 1-thio-β-d-galactopyranoside	Glu200	Glu298	[39]
GH36	D	(β/α)8	alpha-d	retaining	anti	4fns	β-galactosidase	Geobacillus stearothermophilus	1-deoxy galactonojirimycin	Asp584	Asp478	[40]
GH37	G	(α/α)6	alpha-d	inverting	anti	2jf4	trehalase	Escherichia coli	validoxylamine	Asp312	Glu496	[41]
GH38	none	(β/α)7	alpha-d	retaining	anti	3czn	Golgi α-mannosidase II	Drosophila melanogaster	GlcNAcMan(5)GlcNAc(2)	Asp341	Asp204	[42]
GH39	A	(β/α)8	beta-d / alpha-l	retaining	anti	2bfg	β-xylosidase	Geobacillus stearothermophilus	2,5-dinitrophenyl-β-d-xyloside	Glu160	Glu278	[43]
GH42	A	(β/α)8	beta-d / alpha-l	retaining	anti	4ucf	β-galactosidase	Bifidobacterium bifidum	d-galactose	Glu161	Glu320	[44]
GH43	F	5-fold β-propeller	beta-d / alpha-l	inverting	anti	3akh	exo-1,5-α-l-arabinofuranosidase	Streptomyces avermitilis	α-1,5-arabinofuranotriose	Glu196	Asp220	[45]
GH44	none	(β/α)8	beta-d	retaining	anti	2eqd	endoglucanase	Clostridium thermocellum	cellooctaose	Glu186	Glu359	[46]
GH45	none	6-stranded β-barrel	beta-d	inverting	syn	4eng	endo-1,4-glucanase	Humicola insolens	cellohexaose	Asp121	Asp10	[47]
GH46	I	lysozyme type	beta-d	inverting	syn	4olt	chitosanase	Microbacterium sp. OU01	hexa-glucosamine	Glu25	Asp43	[48]
GH47	none	(α/α)7	alpha-d	inverting	anti	1x9d	α-mannosidase I	Homo sapiens	Me-2-S-(α-Man)-2-thio-α-Man	Asp463	Glu599	[49], [50]
GH48	M	(α/α)6	beta-d	inverting	predicted anti by clan	see at GH8
GH49	N	β-helix	alpha-d	inverting	predicted anti by clan	see at GH28
GH50	A	(β/α)8	beta-d	retaining	anti	4bq5	exo-β-agarase	Saccharophagus degradans	neoagarotetraose	Glu535	Glu695	[51]
GH51	A	(β/α)8	beta-d / alpha-l	retaining	anti	1qw9	α-l-arabinofuranosidase	Geobacillus stearothermophilus	PNP-l-arabinofuranoside	Glu175	Glu294	[52]
GH52	O	(α/α)6	beta-d	retaining	anti	4c1p	β-xylosidase	Geobacillus thermoglucosidasius	xylobiose	Asp517	Glu537	[53]
GH53	A	(β/α)8	beta-d	retaining	anti	2ccr	β-1,4-galactanase	Bacillus licheniformis	galactotriose	Glu165	Glu263	[54]
GH54	none	β-sandwich	beta-d / alpha-l	retaining	anti	1wd4	α-l-arabinofuranosidase B	Aspergillus kawachii	l-arabinofuranose	Asp297	Glu221	[55]
GH55	none	β-helix	beta-d	inverting	syn	4tz5	exo-β-1,3-glucanase	Streptomyces sp. SirexAA-E	laminarihexaose	Glu502	unknown	[56]
GH56	none	(β/α)7	beta-d	retaining	anti	1fcv	hyaluronidase	Apis mellifera	(hyaluron.)4	Glu113	internal	[57]
GH57	none	(β/α)7	alpha-d	retaining	anti	1k1y	glucanotransferase	Thermococcus litoralis	acarbose	Asp214	Glu123	[58]
GH59	A	(β/α)8	beta-d	retaining	anti	4ccc	β-galactocerebrosidase	Mus musculus	PNP-β-d-galactoside	Glu182	Glu258	[59]
GH62	F	5-fold β-propeller	alpha-l	inverting	anti	3wn0	α-l-arabinofuranosidase	Streptomyces coelicolor	β-l-Arabinofuranose	Glu361	Asp202	[60]
GH63	G	(α/α)6	alpha-d	inverting	anti	5ca3	α-glucosidase	Escherichia coli	glucose and lactose	Asp501	Glu727	[61]
GH65	L	(α/α)6	alpha-d (and α-l-rham)	inverting	anti	4ktr	2-O-α-glucosylglycerol phosphorylase	Bacillus selenitireducens	isofagomine	Glu475	phosphate	[62]
GH66	none	(β/α)8	alpha-d	retaining	anti	5axh	dextranase	Thermoanaerobacter pseudethanolicus	isomaltohexaose	Glu374	Asp312	[63]
GH67	none	(β/α)8	alpha-d	inverting	syn	1l8n	α-glucuronidase	Geobacillus stearothermophilus	4-O-methyl-d-glucuronic acid and xylotriose	Glu286	Asp364 Glu392	[64]
GH68	J	5-fold β-propeller	beta-d	retaining	anti	1pt2	levansucrase	Bacillus subtilis	sucrose	Glu342	Asp86	[65]
GH70	H	(β/α)8	alpha-d	retaining	anti	3aic	glucansucrase	Streptococcus mutans	α-acarbose	Glu515	Asp477	[66]
GH72	A	(β/α)8	beta-d	retaining	anti	2w62	β-1,3-glucanotransferase	Saccharomyces cerevisiae S288C	laminaripentaose	Glu176	Glu275	[67]
GH74	none	7-fold β-propeller	beta-d	inverting	syn	2ebs	cellobiohydrolase (OXG-RCBH)	Geotrichum sp. m128	xyloglucan heptasaccharide	Asp465	Asp35	[68]
GH76	none	(α/α)6	alpha-d	retaining	anti	5agd	endo-α-1,6-mannanase	Bacillus circulans	α-1,6-mannopentaose	Asp125	Asp124	[69]
GH77	H	(β/α)8	alpha-d	retaining	anti	2oww	4-α-glucanotransferase	Thermus thermofilus	acarbose + 4-deoxy-α-d-glucose	Glu340	Asp293	[70]
GH78	H	(α/α)6	alpha-l	inverting	anti	3w5n	α-l-rhamnosidase	Streptomyces avermitilis	l-rhamnose	Glu636	Glu895	[71]
GH79	A	(β/α)8	beta-d	retaining	anti	5e9c	heparanase	Homo sapiens	heparin tetrasaccharide	Glu225	Glu343	[72]
GH80	I	α + β	beta-d	inverting	predicted syn by clan	see at GH24
GH81	none	β-sandwich	beta-d	inverting	syn	5t4g	endo-β-1,3-glucanase	Bacillus halodurans C-125	laminarin	Asp466	Glu542	[73]
GH83	E	6-fold β-propeller	alpha-d	retaining	predicted anti by clan	see e.g. at GH33
GH84	none	(β/α)8	beta-d	retaining	anti	2chn	β-N-acetyl-glucosaminidase	Bacteroides thetaiotaomicron VPI-5482	NAG-thiazoline	Glu242	internal	[74]
GH85	K	(β/α)8	beta-d	retaining	anti	2w92	endo-β-N-acetyl-glucosaminidase D	Streptococcus pneumoniae TIGR4	NAG-thiazoline	Glu337	internal	[75]
GH86	A	(β/α)8	beta-d	retaining	anti	4aw7	β-porphyranase	Bacteroides plebeius	porphyran fragment	Glu152	Glu279	[76]
GH89	none	(β/α)8	alpha-d	retaining	anti	2vcb	α-N-acetyl-glucosaminidase	Clostridium perfringens	PUGNAc	Glu483	Glu601	[77]
GH92	none	(α/α)6 and β-sandwich	alpha-d	inverting	anti	2ww1	α-1,2-mannosidase	Bacteroides thetaiotaomicron VPI-5482	thiomannobioside	Glu533	Asp644 Asp642	[78]
GH93	E	6-fold β-propeller	alpha-l	retaining	anti	3a72	exo-arabinanase	Penicillium chrysogenum	arabinobiose	Glu246	Glu174	[79]
GH94	Q	(α/α)6	beta-d	inverting	syn	4zli	cellobionic acid phosphorylase	Saccharophagus degradans	3-O-β-d-glucopyranosyl-α-d-glucopyranuronic acid	Asp472	phosphate	[80]
GH95	none	(α/α)6	alpha-l	inverting	anti	2ead	α-1,2-l-fucosidase	Bifidobacterium bifidum	Fuc-α-1,2-Gal	Glu566	Asn423 Asp766	[81]
GH97	none	(β/α)8	alpha-d	retaining + inverting	anti	2zq0	α-glucosidase	Bacteroides thetaiotaomicron VPI-5482	acarbose	Glu532	Glu508	[82]
GH98	none	(β/α)8 and β-sandwich	beta-d	inverting	anti	2wmg	endo-β-1,4-galactosidase	Streptococcus pneumoniae	A-LewisY pentasaccharide	Glu158	Asp251 Glu301	[83]
GH99	none	(β/α)8	alpha-d	retaining	anti	4ad4	endo-α-mannosidase	Bacteroides xylanisolvens	glucose-1,3-isofagomine and α-1,2- mannobiose	Glu336	debated	[84]
GH100	none	(α/α)6 core	beta-d	inverting	anti	5gop	invertase	Anabaena (Nostoc) sp. pcc7120	sucrose	Asp188	Glu414	[85]
GH102	none	double-ψ β-barrel	beta-d	retaining	syn	2pi8	lytic transglycosylase A	Escherichia coli	chitohexaose	Asp308	none	[86]
GH103	none	lysozyme type	beta-d	retaining	syn	1d0k	lytic transglycosylase SLT35	Escherichia coli	murodipeptides	Glu162	internal	[87]
GH106	none	(β/α)8	alpha-l	inverting	anti	5mwk	α-l-rhamnosidase BT_0986	Bacteroides thetaiotaomicron	pectin heptasaccharide	Glu461	Glu593 or Glu561	[88]
GH107	R	(β/α)8	alpha-l	retaining	predicted syn by clan	see at GH29
GH113	A	(β/α)8	beta-d	retaining	anti	4cd8	β-mannanase	Alicyclobacillus acidocaldarius	mannobioimidazole	Glu151	Glu231	[89]
GH116	O	(α/α)6 and β-sandwich	beta-d	retaining	predicted anti by clan	see at GH52
GH117	none	5-fold β-propeller	alpha-l	inverting	anti	4ak7	α-1,3-3,6-anhydro-l-galactosidase	Bacteroides plebeius	neoagarobiose	His302	Asp90	[90]
GH120	none	parallel β-helix and β-sandwich	beta-d	retaining	anti	3vsv	β-xylosidase XylC	Thermoanaerobacterium saccharolyticum JW/SL-YS485	d-xylose	Glu405	Asp382	[91]
GH123	none	(β/α)8 and β-sandwich	beta-d	retaining	anti	5fr0	exo-β-N-acetyl-galactosaminidase	Clostridium perfringens	N-difluoroacetyl-d-galactosamine	Glu345	internal	[92]
GH125	L	(α/α)6	alpha-d	inverting	anti	5m7y	exo-α-1,6-mannosidase	Clostridium perfringens	1,6-α-mannotriose	Asp220	Glu393	[93]
GH127	P	(α/α)6 and β-sandwich	beta-l	retaining	anti	3wrg	β-l-arabinofuranosidase	Bifidobacterium longum	l-arabinose	Glu322	Cys417	[94]
GH128	A	(β/α)8	beta-d	retaining	predicted anti by clan	see e.g. at GH1
GH130	none	5-fold β-propeller	beta-d	inverting	anti	5b0s	β-1,2-mannobiose phosphorylase	Listeria innocua	β-1,2-mannotriose	Asp141 relay	phosphate	[95]
GH134	none	β + α	beta-d	inverting	syn	5jug	β-mannanase	Streptomyces sp.	mannopentaose	Glu45	Asp57	[96]
GH136	none	β-helix	beta-d	retaining	syn	5gqf	lacto-N-biosidase	Bifidobacterium longum	lacto-N-biose	Asp411	Asp418	[97]
GH137	none	5-fold β-propeller	beta-l	unknown	anti	5mui	β-l-arabinofuranosidase BT_0996	Bacteroides thetaiotaomicron	pectin oligosaccharide	Glu240	Glu159	[88]
GH138	none	(β/α)8	alpha-d	retaining	syn	6hzg	α-1,2-d-galacturonidase	Bacteroides paurosaccharolyticus	alpha-d-galactopyranuronic	Glu294	Glu361	[98]
GH146	P	(α/α)6 and β-sandwich	beta-l	retaining	anti	5opj	β-l-arabinofuranosidase BT_0349	Bacteroides thetaiotaomicron	l-arabinose	Glu320	Cys416	[99]
GH147	A	(β/α)8	beta-d	retaining	predicted anti by clan	see at e.g. GH1
GH148	A	(β/α)8	beta-d	retaining	predicted anti by clan	see at e.g. GH1
GH149	Q	(α/α)6	beta-d	inverting	predicted syn by clan	see at GH94
GH157	A	(β/α)8	beta-d	retaining	predicted anti by clan	see at e.g. GH1
GH158	A	(β/α)8	beta-d	retaining	predicted anti by clan	see at e.g. GH1
GH161	Q	(α/α)6	beta-d	retaining	predicted syn by clan	see at GH94
GH162	none	(α/α)6	beta-d	inverting	syn	5imw	endo-β-1,2-glucanase	Talaromyces funiculosus	beta-1,2-glucan	Glu262	Asp446	[100]
n.c.*	none	parallel β-helix	alpha-d	inverting	anti	2vjj	endo-α-N-acetylglucosaminidase	Bacteriophage HK620	O18A1 O-antigen hexasaccharide	Asp339	Glu372	[101]

* n.c.: Found among the collection of non-classified GH sequences in the CAZy Database.

References

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