Glycoside Hydrolase Family 76

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• Author: Spencer Williams
• Responsible Curators: Gideon Davies and Harry Gilbert

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Glycoside Hydrolase Family GH76
Clan	not assigned
Mechanism	retaining
Active site residues	known
CAZy DB link
https://www.cazy.org/GH76.html

Substrate specificities

Glycoside hydrolases of family GH76 are endo-acting α-mannanases. GH76 genes are found within bacteria and fungi. Bacterial GH76 enzymes cleave α-1,6-mannans, such as those found within the α-1,6-linked backbone of fungal mannoproteins and mycobacterial cell wall lipomannan, lipoarabinomannan and phosphatidylinositol mannosides. This family was originally created from the cloning and characterization of Aman6 from Bacillus circulans TN-31 [1], which appears to be the same enzyme as that characterized much earlier by Ballou and co-workers [2]. A related protein, Emn, has been cloned from Bacillus circulans TN-31 genomic DNA [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16]; mannotriose is the minimum substrate for the enzyme [2]. A possible GH76 enzyme has been detected within Mycobacterium smegmatis, which has the capacity to degrade α-1,6-mannooligosaccharides [17].

Additional characterized GH76 enzymes include several from the gut bacterium Bacteroides thetaiotaomicron [18] and ShGH76 from the marine bacterium Salegentibacter sp Hel_I_6 [5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 16, 19, 19, 20, 20, 21, 22, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 25, 26, 27, 27, 27, 27, 27, 27, 28, 29, 30, 31, 32, 33, 33, 33, 34, 35, 36, 37, 38, 38, 39, 39, 40, 41, 42, 43, 44, 44, 45, 46, 47, 48, 48, 48, 48, 48, 49, 50, 51, 52, 53, 54, 55, 55, 56, 56, 56, 57, 58, 59, 60, 61, 62, 63, 64, 64, 64, 65, 65, 66, 66, 67, 67, 68, 69, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105]. DFG-5 from Neurospora crassa has an enzymatic activity and processes the α-1,6-mannose backbone of fungal N-linked galactomannan [5, 5, 5, 5, 8, 9, 9, 11, 11, 12, 12, 14, 14, 14, 14, 16, 18, 20, 23, 24, 27, 56, 63, 64, 64, 86, 86, 101, 101, 101, 103, 106, 107, 107, 107, 107, 108, 109, 109, 109, 110, 111, 112, 113, 113, 114, 115, 116, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142]. GH76 enzymes are believed to proceed through a classical Koshland double-displacement mechanism. Crystallographic evidence from a binary complexes of the catalytic domain of Bacillus circulans Aman6 with substrate and inhibitors, complemented by quantum mechanics/molecular mechanics calculations of preferred conformations on-enzyme supports a ¹S₅→B_2,5^‡→^OS₂ conformational reaction coordinate [143].

Catalytic Residues

Inspection of the X-ray structure of Bacteroides thetaiotaomicron BT3792 revealed two consecutive asparate residues, D258 and D259, that were predicted to be catalytic residues [18]. The equivalent pair of conserved aspartic acid residues (D124 and D125 in the catalytic domain of Bacillus circulans Aman6) were identified as catalytic nucleophile and general acid/base, respectively, based on X-ray analysis of substrate and inhibitor complexes, dovetailed with kinetic analysis of mutants [143].

Three-dimensional structures

Three-dimensional structures are available for several bacterial members of GH76, including the catalytic domain of Bacillus circulans Aman6, Bacteroides thetaiotaomicron BT2949 and BT3792, Listeria innocua Clip11262 and Salegentibacter sp. Hel_I_6 ShGH76 (see the GH76 structure page in the CAZy Database). They have an (α/α)₆ fold. A complex of mannopentaose bound in the active site of Bacillus circulans GH76 defined the -4 to +1 subsites, and showed the sugar binding in the -1 subsite in a ¹S₅ conformation. A complex of the same enzyme with α-1,6-mannobiose showed the disaccharide binding in the -3/-2 subsites (unpublished, PDB ID 4boj). Several inhibtior complezes have been reported. A complex with the inhibitor α-mannosyl-1,6-isofagomine revealed the inhibtior to bind in the -2/-1 subsites and displayed the isofagomine ring in a B_2,5 conformation, with the nitrogen of the inhibitor hydrogen-bonded to the nucleophile (D124) [143]. The S-linked analogue α-mannosyl-1,6-S-isofagomine (ManSIFG) bound with similar affinity to the enzyme and also in the -2/-1 subsites, but instead the inhibitor bound in a relaxed ⁴C₁ conformation with the inhibitor nitrogen hydrogen bonded to the acid/base (D125) [144].

Family Firsts

First stereochemistry determination

Bacteroides thetaiotaomicron α-1,6-mannanase by ¹H NMR [18]

First catalytic nucleophile identification

D124 for Bacillus circulans catalytic domain [143].

First general acid/base residue identification

D125 for Bacillus circulans catalytic domain [143].

First 3-D structure of a GH76 enzyme

Listeria innocua Lin0763 (unpublished, PDB ID 3k7x)

References

1. Maruyama Y and Nakajima T. (2000). The aman6 gene encoding a yeast mannan backbone degrading 1,6-alpha-D-mannanase in Bacillus circulans: cloning, sequence analysis, and expression. Biosci Biotechnol Biochem. 2000;64(9):2018-20. DOI:10.1271/bbb.64.2018 |
2. Nakajima T, Maitra SK, and Ballou CE. (1976). An endo-alpha1 leads to 6-D-mannanase from a soil bacterium. Purification, properties, and mode of action. J Biol Chem. 1976;251(1):174-81. | Google Books | Open Library
17. Yokoyama K and Ballou CE. (1989). Synthesis of alpha 1----6-mannooligosaccharides in Mycobacterium smegmatis. Function of beta-mannosylphosphoryldecaprenol as the mannosyl donor. J Biol Chem. 1989;264(36):21621-8. | Google Books | Open Library
18. Cuskin F, Lowe EC, Temple MJ, Zhu Y, Cameron E, Pudlo NA, Porter NT, Urs K, Thompson AJ, Cartmell A, Rogowski A, Hamilton BS, Chen R, Tolbert TJ, Piens K, Bracke D, Vervecken W, Hakki Z, Speciale G, Munōz-Munōz JL, Day A, Peña MJ, McLean R, Suits MD, Boraston AB, Atherly T, Ziemer CJ, Williams SJ, Davies GJ, Abbott DW, Martens EC, and Gilbert HJ. (2015). Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature. 2015;517(7533):165-169. DOI:10.1038/nature13995 |
105. Kitagaki H, Wu H, Shimoi H, and Ito K. (2002). Two homologous genes, DCW1 (YKL046c) and DFG5, are essential for cell growth and encode glycosylphosphatidylinositol (GPI)-anchored membrane proteins required for cell wall biogenesis in Saccharomyces cerevisiae. Mol Microbiol. 2002;46(4):1011-22. DOI:10.1046/j.1365-2958.2002.03244.x |
143. Thompson AJ, Speciale G, Iglesias-Fernández J, Hakki Z, Belz T, Cartmell A, Spears RJ, Chandler E, Temple MJ, Stepper J, Gilbert HJ, Rovira C, Williams SJ, and Davies GJ. (2015). Evidence for a boat conformation at the transition state of GH76 α-1,6-mannanases--key enzymes in bacterial and fungal mannoprotein metabolism. Angew Chem Int Ed Engl. 2015;54(18):5378-82. DOI:10.1002/anie.201410502 |
144. Belz T, Jin Y, Coines J, Rovira C, Davies GJ, and Williams SJ. (2017). An atypical interaction explains the high-affinity of a non-hydrolyzable S-linked 1,6-α-mannanase inhibitor. Chem Commun (Camb). 2017;53(66):9238-9241. DOI:10.1039/c7cc04977c |
145. Angala SK, Li W, Palčeková Z, Zou L, Lowary TL, McNeil MR, and Jackson M. (2019). Cloning and Partial Characterization of an Endo-α-(1→6)-d-Mannanase Gene from Bacillus circulans. Int J Mol Sci. 2019;20(24). DOI:10.3390/ijms20246244 |
146. Solanki V, Krüger K, Crawford CJ, Pardo-Vargas A, Danglad-Flores J, Hoang KLM, Klassen L, Abbott DW, Seeberger PH, Amann RI, Teeling H, and Hehemann JH. (2022). Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi. ISME J. 2022;16(7):1818-1830. DOI:10.1038/s41396-022-01223-w |
147. Patel PK, Tung SK, Porfirio S, Sonon R, Azadi P, and Free SJ. (2022). Extracellular targeting of Neurospora crassa cell wall and secreted glycoproteins by DFG-5. Fungal Genet Biol. 2022;160:103686. DOI:10.1016/j.fgb.2022.103686 |