6CVM
Atomic resolution cryo-EM structure of beta-galactosidase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| A | 0004565 | molecular_function | beta-galactosidase activity |
| A | 0005975 | biological_process | carbohydrate metabolic process |
| A | 0005990 | biological_process | lactose catabolic process |
| A | 0009056 | biological_process | catabolic process |
| A | 0009341 | cellular_component | beta-galactosidase complex |
| A | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| A | 0030246 | molecular_function | carbohydrate binding |
| A | 0031420 | molecular_function | alkali metal ion binding |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| B | 0004565 | molecular_function | beta-galactosidase activity |
| B | 0005975 | biological_process | carbohydrate metabolic process |
| B | 0005990 | biological_process | lactose catabolic process |
| B | 0009056 | biological_process | catabolic process |
| B | 0009341 | cellular_component | beta-galactosidase complex |
| B | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| B | 0030246 | molecular_function | carbohydrate binding |
| B | 0031420 | molecular_function | alkali metal ion binding |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| C | 0004565 | molecular_function | beta-galactosidase activity |
| C | 0005975 | biological_process | carbohydrate metabolic process |
| C | 0005990 | biological_process | lactose catabolic process |
| C | 0009056 | biological_process | catabolic process |
| C | 0009341 | cellular_component | beta-galactosidase complex |
| C | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| C | 0030246 | molecular_function | carbohydrate binding |
| C | 0031420 | molecular_function | alkali metal ion binding |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| D | 0004565 | molecular_function | beta-galactosidase activity |
| D | 0005975 | biological_process | carbohydrate metabolic process |
| D | 0005990 | biological_process | lactose catabolic process |
| D | 0009056 | biological_process | catabolic process |
| D | 0009341 | cellular_component | beta-galactosidase complex |
| D | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| D | 0030246 | molecular_function | carbohydrate binding |
| D | 0031420 | molecular_function | alkali metal ion binding |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 16 |
| Details | binding site for residue PTQ A 2001 |
| Chain | Residue |
| A | ASN102 |
| A | ASP598 |
| A | PHE601 |
| A | VAL795 |
| A | TRP999 |
| A | NA2004 |
| A | HOH2136 |
| A | HOH2283 |
| A | ASP201 |
| A | HIS391 |
| A | GLU461 |
| A | MET502 |
| A | TYR503 |
| A | GLU537 |
| A | HIS540 |
| A | TRP568 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 2002 |
| Chain | Residue |
| A | GLU416 |
| A | HIS418 |
| A | GLU461 |
| A | HOH2136 |
| A | HOH2226 |
| A | HOH2283 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 2003 |
| Chain | Residue |
| A | ASP15 |
| A | ASN18 |
| A | VAL21 |
| A | GLN163 |
| A | ASP193 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 2004 |
| Chain | Residue |
| A | TYR100 |
| A | ASP201 |
| A | PHE601 |
| A | ASN604 |
| A | PTQ2001 |
| A | HOH2633 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 2005 |
| Chain | Residue |
| A | PHE556 |
| A | TYR559 |
| A | PRO560 |
| A | LEU562 |
| A | HOH2432 |
| A | HOH2643 |
| site_id | AC6 |
| Number of Residues | 16 |
| Details | binding site for residue PTQ B 2001 |
| Chain | Residue |
| B | ASN102 |
| B | ASP201 |
| B | HIS391 |
| B | GLU461 |
| B | MET502 |
| B | TYR503 |
| B | GLU537 |
| B | HIS540 |
| B | TRP568 |
| B | ASP598 |
| B | PHE601 |
| B | VAL795 |
| B | TRP999 |
| B | NA2004 |
| B | HOH2139 |
| B | HOH2282 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 2002 |
| Chain | Residue |
| B | GLU416 |
| B | HIS418 |
| B | GLU461 |
| B | HOH2139 |
| B | HOH2227 |
| B | HOH2282 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 2003 |
| Chain | Residue |
| B | ASP15 |
| B | ASN18 |
| B | VAL21 |
| B | GLN163 |
| B | ASP193 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 2004 |
| Chain | Residue |
| B | TYR100 |
| B | ASP201 |
| B | PHE601 |
| B | ASN604 |
| B | PTQ2001 |
| B | HOH2633 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 2005 |
| Chain | Residue |
| B | PHE556 |
| B | TYR559 |
| B | PRO560 |
| B | LEU562 |
| B | HOH2432 |
| B | HOH2643 |
| site_id | AD2 |
| Number of Residues | 16 |
| Details | binding site for residue PTQ C 2001 |
| Chain | Residue |
| C | ASN102 |
| C | ASP201 |
| C | HIS391 |
| C | GLU461 |
| C | MET502 |
| C | TYR503 |
| C | GLU537 |
| C | HIS540 |
| C | TRP568 |
| C | ASP598 |
| C | PHE601 |
| C | VAL795 |
| C | TRP999 |
| C | NA2004 |
| C | HOH2139 |
| C | HOH2283 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 2002 |
| Chain | Residue |
| C | HOH2283 |
| C | GLU416 |
| C | HIS418 |
| C | GLU461 |
| C | HOH2139 |
| C | HOH2225 |
| site_id | AD4 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 2003 |
| Chain | Residue |
| C | ASP15 |
| C | ASN18 |
| C | VAL21 |
| C | GLN163 |
| C | ASP193 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue NA C 2004 |
| Chain | Residue |
| C | TYR100 |
| C | ASP201 |
| C | PHE601 |
| C | ASN604 |
| C | PTQ2001 |
| C | HOH2634 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue NA C 2005 |
| Chain | Residue |
| C | PHE556 |
| C | TYR559 |
| C | PRO560 |
| C | LEU562 |
| C | HOH2433 |
| C | HOH2644 |
| site_id | AD7 |
| Number of Residues | 16 |
| Details | binding site for residue PTQ D 2001 |
| Chain | Residue |
| D | ASN102 |
| D | ASP201 |
| D | HIS391 |
| D | GLU461 |
| D | MET502 |
| D | TYR503 |
| D | GLU537 |
| D | HIS540 |
| D | TRP568 |
| D | ASP598 |
| D | PHE601 |
| D | VAL795 |
| D | TRP999 |
| D | NA2004 |
| D | HOH2135 |
| D | HOH2281 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 2002 |
| Chain | Residue |
| D | GLU416 |
| D | HIS418 |
| D | GLU461 |
| D | HOH2135 |
| D | HOH2225 |
| D | HOH2281 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue MG D 2003 |
| Chain | Residue |
| D | ASP15 |
| D | ASN18 |
| D | VAL21 |
| D | GLN163 |
| D | ASP193 |
| site_id | AE1 |
| Number of Residues | 6 |
| Details | binding site for residue NA D 2004 |
| Chain | Residue |
| D | TYR100 |
| D | ASP201 |
| D | PHE601 |
| D | ASN604 |
| D | PTQ2001 |
| D | HOH2633 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue NA D 2005 |
| Chain | Residue |
| D | PHE556 |
| D | TYR559 |
| D | PRO560 |
| D | LEU562 |
| D | HOH2433 |
| D | HOH2644 |
Functional Information from PROSITE/UniProt
| site_id | PS00608 |
| Number of Residues | 15 |
| Details | GLYCOSYL_HYDROL_F2_2 Glycosyl hydrolases family 2 acid/base catalyst. DRNHPSVIIWSlg.NE |
| Chain | Residue | Details |
| A | ASP447-GLU461 |
| site_id | PS00719 |
| Number of Residues | 26 |
| Details | GLYCOSYL_HYDROL_F2_1 Glycosyl hydrolases family 2 signature 1. NaVRCSHYPnhplWYtlcDryGLYVV |
| Chain | Residue | Details |
| A | ASN385-VAL410 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor => ECO:0000269|PubMed:6420154 |
| Chain | Residue | Details |
| A | GLU461 | |
| B | GLU461 | |
| C | GLU461 | |
| D | GLU461 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Nucleophile => ECO:0000269|PubMed:1350782 |
| Chain | Residue | Details |
| A | GLU537 | |
| B | GLU537 | |
| C | GLU537 | |
| D | GLU537 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 28 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ASN102 | |
| B | GLU461 | |
| B | GLU537 | |
| B | PHE601 | |
| B | ASN604 | |
| B | TRP999 | |
| C | ASN102 | |
| C | ASP201 | |
| C | GLU461 | |
| C | GLU537 | |
| C | PHE601 | |
| A | ASP201 | |
| C | ASN604 | |
| C | TRP999 | |
| D | ASN102 | |
| D | ASP201 | |
| D | GLU461 | |
| D | GLU537 | |
| D | PHE601 | |
| D | ASN604 | |
| D | TRP999 | |
| A | GLU461 | |
| A | GLU537 | |
| A | PHE601 | |
| A | ASN604 | |
| A | TRP999 | |
| B | ASN102 | |
| B | ASP201 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11045615 |
| Chain | Residue | Details |
| A | GLU416 | |
| D | GLU416 | |
| D | HIS418 | |
| D | ASN597 | |
| A | HIS418 | |
| A | ASN597 | |
| B | GLU416 | |
| B | HIS418 | |
| B | ASN597 | |
| C | GLU416 | |
| C | HIS418 | |
| C | ASN597 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | SITE: Transition state stabilizer |
| Chain | Residue | Details |
| A | HIS357 | |
| A | HIS391 | |
| B | HIS357 | |
| B | HIS391 | |
| C | HIS357 | |
| C | HIS391 | |
| D | HIS357 | |
| D | HIS391 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | SITE: Important for ensuring that an appropriate proportion of lactose is converted to allolactose |
| Chain | Residue | Details |
| A | TRP999 | |
| B | TRP999 | |
| C | TRP999 | |
| D | TRP999 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 10 |
| Details | M-CSA 422 |
| Chain | Residue | Details |
| A | ASP201 | |
| A | ASN604 | |
| A | HIS357 | |
| A | HIS391 | |
| A | GLU416 | |
| A | HIS418 | |
| A | GLU461 | |
| A | GLU537 | |
| A | ASN597 | |
| A | PHE601 |
| site_id | MCSA2 |
| Number of Residues | 10 |
| Details | M-CSA 422 |
| Chain | Residue | Details |
| B | ASP201 | |
| B | ASN604 | |
| B | HIS357 | |
| B | HIS391 | |
| B | GLU416 | |
| B | HIS418 | |
| B | GLU461 | |
| B | GLU537 | |
| B | ASN597 | |
| B | PHE601 |
| site_id | MCSA3 |
| Number of Residues | 10 |
| Details | M-CSA 422 |
| Chain | Residue | Details |
| C | ASP201 | |
| C | ASN604 | |
| C | HIS357 | |
| C | HIS391 | |
| C | GLU416 | |
| C | HIS418 | |
| C | GLU461 | |
| C | GLU537 | |
| C | ASN597 | |
| C | PHE601 |
| site_id | MCSA4 |
| Number of Residues | 10 |
| Details | M-CSA 422 |
| Chain | Residue | Details |
| D | ASP201 | |
| D | ASN604 | |
| D | HIS357 | |
| D | HIS391 | |
| D | GLU416 | |
| D | HIS418 | |
| D | GLU461 | |
| D | GLU537 | |
| D | ASN597 | |
| D | PHE601 |
