6Y8F

An inactive (D136N and D137N) variant of alpha-1,6-mannanase, GH76A of Salegentibacter sp. HEL1_6 in complex with alpha-1,6-mannotriose

Summary for 6Y8F

• Entry DOI: 10.2210/pdb6y8f/pdb
• Descriptor: Alpha-1,6-endo-mannanase GH76A mutant, alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: glycoside hydrolase, gh76, mannan, cazymes, mannanases, hydrolase
• Biological source: Salegentibacter sp. Hel_I_6
• Total number of polymer chains: 1
• Total formula weight: 44501.41

Authors

Hehemann, J.H.,Solanki, V.A. (deposition date: 2020-03-04, release date: 2021-03-31, Last modification date: 2024-01-24)

Primary citation

Solanki, V.,Kruger, K.,Crawford, C.J.,Pardo-Vargas, A.,Danglad-Flores, J.,Hoang, K.L.M.,Klassen, L.,Abbott, D.W.,Seeberger, P.H.,Amann, R.I.,Teeling, H.,Hehemann, J.H.
Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi.
Isme J, 2022

PubMed Abstract: Microbial glycan degradation is essential to global carbon cycling. The marine bacterium Salegentibacter sp. Hel_I_6 (Bacteroidota) isolated from seawater off Helgoland island (North Sea) contains an α-mannan inducible gene cluster with a GH76 family endo-α-1,6-mannanase (ShGH76). This cluster is related to genetic loci employed by human gut bacteria to digest fungal α-mannan. Metagenomes from the Hel_I_6 isolation site revealed increasing GH76 gene frequencies in free-living bacteria during microalgae blooms, suggesting degradation of α-1,6-mannans from fungi. Recombinant ShGH76 protein activity assays with yeast α-mannan and synthetic oligomannans showed endo-α-1,6-mannanase activity. Resolved structures of apo-ShGH76 (2.0 Å) and of mutants co-crystalized with fungal mannan-mimicking α-1,6-mannotetrose (1.90 Å) and α-1,6-mannotriose (1.47 Å) retained the canonical (α/α) fold, despite low identities with sequences of known GH76 structures (GH76s from gut bacteria: <27%). The apo-form active site differed from those known from gut bacteria, and co-crystallizations revealed a kinked oligomannan conformation. Co-crystallizations also revealed precise molecular-scale interactions of ShGH76 with fungal mannan-mimicking oligomannans, indicating adaptation to this particular type of substrate. Our data hence suggest presence of yet unknown fungal α-1,6-mannans in marine ecosystems, in particular during microalgal blooms.

PubMed: 35414716
DOI: 10.1038/s41396-022-01223-w

Experimental method

X-RAY DIFFRACTION (1.472 Å)