New to the CAZy classification? Read this first.
Want to learn more about CAZypedia? Read the CAZypedia 10th anniversary article in Glycobiology.

Glycoside Hydrolase Family 76

From CAZypedia
Jump to navigation Jump to search
Approve icon-50px.png

This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.



Glycoside Hydrolase Family GH76
Clan not assigned
Mechanism retaining
Active site residues known
CAZy DB link
http://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 [3]. Aman6 degrades α-1,6-mannan to a mixture of the mannobiose and mannotriose [1]; 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 [4].

Additional characterized GH76 enzymes include several from the gut bacterium Bacteroides thetaiotaomicron [5] and ShGH76 from the marine bacterium Salegentibacter sp Hel_I_6 [6]. B. thetaiotaomicron expresses numerous GH76 enzymes. Several of these are found within polysaccharide utilization loci that are specifically up-regulated upon exposure to yeast α-mannan. Likewise the Salegentibacter genes reside in PUL-like clusters. These enzymes have the capacity to utilize unadorned linear α-1,6-mannan, but have little activity on highly branched wildtype α-mannan. Certain B. thetaiotaomicron GH76 enzymes are lipoenzymes that are associated with the cell surface, where they appear to act on large yeast mannan molecules that have undergone partial trimming to expose sections of the core α-1,6-mannan. Other periplasmic located GH76 enzymes have activity on shorter α-1,6-mannan fragments, which are obtained by importation of partially-digested fragments arising from the action of cell surface enzymes.

Fungal GH76 enzymes have been speculated to be involved in cross-linking of GPI-anchored proteins into the cell wall, where they are proposed to act as transglycosylases [7]. DFG-5 from Neurospora crassa has an enzymatic activity and processes the α-1,6-mannose backbone of fungal N-linked galactomannan [8]. Cell wall glycoproteins co-purify with DFG-5 indicating a specific association between DFG-5 and cell wall glycoproteins. DFG-5 can discriminate between cell wall and secreted glycoproteins, and does not bind to the N-linked galactomannans on secreted glycoproteins.

Kinetics and Mechanism

Family GH76 endo-α-mannosidases are retaining enzymes, as first shown by 1H NMR analysis of the hydrolysis of 4-nitrophenyl α-mannosyl-1,6-α-mannopyranoside by a Bacteroides thetaiotaomicron α-mannanase [5]. 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 1S5B2,5OS2 conformational reaction coordinate [9].

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 [5]. 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 [9].

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 inhibitor complexes 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 B2,5 conformation, with the nitrogen of the inhibitor hydrogen-bonded to the nucleophile (D124) [9]. 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) [10].

Family Firsts

First stereochemistry determination
Bacteroides thetaiotaomicron α-1,6-mannanase by 1H NMR [5]
First catalytic nucleophile identification
D124 for Bacillus circulans catalytic domain [9].
First general acid/base residue identification
D125 for Bacillus circulans catalytic domain [9].
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 | PubMed ID:11055417 [Maruyama2000]
  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 PubMed ID:811665 [Nakajima1976]
  3. 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 | PubMed ID:31835712 [Angala2019]
  4. 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 PubMed ID:2480954 [Yokoyama1989]
  5. 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 | PubMed ID:25567280 [Cuskin2015]
  6. 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 | PubMed ID:35414716 [Solanki2022]
  7. 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 | PubMed ID:12421307 [Kitagaki2002]
  8. 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 | PubMed ID:35306147 [Patel2022]
  9. 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 | PubMed ID:25772148 [Thompson2015]
  10. 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 | PubMed ID:28766587 [Belz2017]

All Medline abstracts: PubMed