Lactococcus lactis subsp. lactis Dephy 1 β-glucosidase Download PDB file

Protein: Beta-glucosidase 6-phospho-beta-glucosidase

Organism: Lactococcus lactis subsp. lactis Dephy 1

Lenght: 213

UniprotID: U6ET99 (Download sequence)

Template: 3AHX:A (56.76%) | [φ,ψ] plot

Amino acid:

Local position¹:

Global position²:

Conserved > 80%:

Conserved 50-79%:

Secondary structure:

Co-evoluted network:

Mutation predicted:

Co-evolution network³

Residue	Community	Network

¹ Residue Corresponding position in the amino acids sequence.

² We performed multiple alignment between all GH1 beta-glucosidases sequences using Clustal omega (default parameters). We collected the amino acids that appear in more than 50% of the sequences and more than 80% of the sequences.

³ Co-evolution network was generated using PFSTATS and family GH1 sequences obtained from PFAM. Amino acid residues edges represent correlation links between them.

Acid/base catalytic
Conserved (50-79%)
Conserved (> 80%)
Extrapoled mutation
Catalytic pocket (0-6.5Å from ligand)

Extrapoled mutations

| Cellobiose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-4.43	-4.60	-0.17	ΔAffinity < 0	✓
1-3	-4.41	-4.43	-0.02	ΔAffinity < 0	✓
1-10	-4.25	-4.27	-0.02	ΔAffinity < 0	✓

| Glucose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-4.43	-4.00	0.43	ΔAffinity > 0	✓
1-3	-4.41	-3.96	0.45	ΔAffinity > 0	✓
1-10	-3.86	-3.70	0.16	ΔAffinity > 0	✓

Methodology

Comparative modeling

Three-dimensional structures were modeled by homology using MODELLER. Sequences were collected in UniProt. We searched for the E.C. number of beta-glucosidases (3.2.1.21) and collected sequences of family GH1 (~3000). For each sequence, we selected the structure of highest identity using BLAST against the PDB database to be used as a template. Sequences with identity lower than 25% were discarded. 100 models were constructed for each sequence. The best model was selected using the lowest value of the DOPE score. Mutants were modeled using MODELLER's mutation script. The mutations were based on beneficial mutations described in the literature.

Minimization

PDB models were minimized using AMBER tools. We performed 1000 steps of minimization in the vacuum (parameters: imin=1, maxcyc=1000, ncyc=750, cut=10.0, ntb=0, igb=0).

Multiple alignment

We performed multiple alignment using Clustal Omega (default parameters). We used Python scripts to detect conservation.

Docking

We performed docking of glucose (product) and cellobiose (substrate) for wild and mutant beta-glucosidases using AutoDock Vina (parameters: exhaustiveness = 20; num_modes = 10). The box center was defined using the median coordinate of the last atom of the two catalytic glutamates. The experiment was performed in triplicate. We collected ten poses for each docking and analyzed the average of affinity energies predicted by the software for (i) pose 1, (ii) poses 1-3, and (iii) poses 1-10.