Protein:GLB1 |
Protein Summary |
 Gene summary |
| Gene name: GLB1 | ASpdb.0 ID: 2720 | Gene | Gene symbol | GLB1 | Gene ID | 2720 |
| Gene name | galactosidase beta 1 |
| Synonyms | EBP|ELNR1|MPS4B |
| Cytomap | 3p22.3 |
| Type of gene | protein-coding |
| Description | beta-galactosidaseacid beta-galactosidaseelastin binding proteinelastin receptor 1, 67kDalactase |
| Modification date | 20240305 |
| UniProtAcc | P16278 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | GLB1 | GO:0004565 | beta-galactosidase activity | 11927518|24737316 |
| Gene | GLB1 | GO:0005737 | cytoplasm | 11927518 |
| Gene | GLB1 | GO:0005794 | Golgi apparatus | - |
| Gene | GLB1 | GO:0005975 | carbohydrate metabolic process | 11927518 |
| Gene | GLB1 | GO:0043231 | intracellular membrane-bounded organelle | - |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| P16278-1 | P16278-1_3thd_A.pdb | 3THD | X-ray | 1.79 | A | 29 | 647 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| P16278 | GLB1 | P16278-1 | P16278-2 | 677 | 546 | 83 | 244 | Substitution | YVPWNFHEPWPGQYQFSEDHDVEYFLRLAHELGLLVILRPGPYICAEWEMGGLPAWLLEKESILLRSSDPDYLAAVDKWLGVLLPKMKPLLYQNGGPVITVQVENEYGSYFACDFDYLRFLQKRFRHHLGDDVVLFTTDGAHKTFLKCGALQGLYTTVDFGT | LPGSCGQVVGSPSAQDEASPLSEWRASYNSA | 83 | 113 |
| P16278 | GLB1 | P16278-1 | P16278-3 | 677 | 647 | 1 | 30 | Deletion | none | none | 0 | 0 |
| Multiple sequence alignment of our canonical and alternatively spliced GLB1 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of GLB1 |
| UniProt-id | ENSG | ENST | ENSP |
| UniProt-id | NM ID | NP ID |
| Amino acid sequences of our canonical and alternatively spliced GLB1 |
| accession_id | Protein sequence |
| P16278-1 | MPGFLVRILPLLLVLLLLGPTRGLRNATQRMFEIDYSRDSFLKDGQPFRYISGSIHYSRVPRFYWKDRLLKMKMAGLNAIQTYVPWNFHE PWPGQYQFSEDHDVEYFLRLAHELGLLVILRPGPYICAEWEMGGLPAWLLEKESILLRSSDPDYLAAVDKWLGVLLPKMKPLLYQNGGPV ITVQVENEYGSYFACDFDYLRFLQKRFRHHLGDDVVLFTTDGAHKTFLKCGALQGLYTTVDFGTGSNITDAFLSQRKCEPKGPLINSEFY TGWLDHWGQPHSTIKTEAVASSLYDILARGASVNLYMFIGGTNFAYWNGANSPYAAQPTSYDYDAPLSEAGDLTEKYFALRNIIQKFEKV PEGPIPPSTPKFAYGKVTLEKLKTVGAALDILCPSGPIKSLYPLTFIQVKQHYGFVLYRTTLPQDCSNPAPLSSPLNGVHDRAYVAVDGI PQGVLERNNVITLNITGKAGATLDLLVENMGRVNYGAYINDFKGLVSNLTLSSNILTDWTIFPLDTEDAVRSHLGGWGHRDSGHHDEAWA HNSSNYTLPAFYMGNFSIPSGIPDLPQDTFIQFPGWTKGQVWINGFNLGRYWPARGPQLTLFVPQHILMTSAPNTITVLELEWAPCSSDD |
| P16278-2 | MPGFLVRILPLLLVLLLLGPTRGLRNATQRMFEIDYSRDSFLKDGQPFRYISGSIHYSRVPRFYWKDRLLKMKMAGLNAIQTLPGSCGQV VGSPSAQDEASPLSEWRASYNSAGSNITDAFLSQRKCEPKGPLINSEFYTGWLDHWGQPHSTIKTEAVASSLYDILARGASVNLYMFIGG TNFAYWNGANSPYAAQPTSYDYDAPLSEAGDLTEKYFALRNIIQKFEKVPEGPIPPSTPKFAYGKVTLEKLKTVGAALDILCPSGPIKSL YPLTFIQVKQHYGFVLYRTTLPQDCSNPAPLSSPLNGVHDRAYVAVDGIPQGVLERNNVITLNITGKAGATLDLLVENMGRVNYGAYIND FKGLVSNLTLSSNILTDWTIFPLDTEDAVRSHLGGWGHRDSGHHDEAWAHNSSNYTLPAFYMGNFSIPSGIPDLPQDTFIQFPGWTKGQV WINGFNLGRYWPARGPQLTLFVPQHILMTSAPNTITVLELEWAPCSSDDPELCAVTFVDRPVIGSSVTYDHPSKPVEKRLMPPPPQKNKD |
| P16278-3 | MFEIDYSRDSFLKDGQPFRYISGSIHYSRVPRFYWKDRLLKMKMAGLNAIQTYVPWNFHEPWPGQYQFSEDHDVEYFLRLAHELGLLVIL RPGPYICAEWEMGGLPAWLLEKESILLRSSDPDYLAAVDKWLGVLLPKMKPLLYQNGGPVITVQVENEYGSYFACDFDYLRFLQKRFRHH LGDDVVLFTTDGAHKTFLKCGALQGLYTTVDFGTGSNITDAFLSQRKCEPKGPLINSEFYTGWLDHWGQPHSTIKTEAVASSLYDILARG ASVNLYMFIGGTNFAYWNGANSPYAAQPTSYDYDAPLSEAGDLTEKYFALRNIIQKFEKVPEGPIPPSTPKFAYGKVTLEKLKTVGAALD ILCPSGPIKSLYPLTFIQVKQHYGFVLYRTTLPQDCSNPAPLSSPLNGVHDRAYVAVDGIPQGVLERNNVITLNITGKAGATLDLLVENM GRVNYGAYINDFKGLVSNLTLSSNILTDWTIFPLDTEDAVRSHLGGWGHRDSGHHDEAWAHNSSNYTLPAFYMGNFSIPSGIPDLPQDTF IQFPGWTKGQVWINGFNLGRYWPARGPQLTLFVPQHILMTSAPNTITVLELEWAPCSSDDPELCAVTFVDRPVIGSSVTYDHPSKPVEKR |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| GLB1 (go to UniProt):P16278 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
Gene Isoform Structures and Expression Levels for GLB1 |
| Gene structures of our canonical and alternative spliced genes of GLB1 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of P16278-1 |
| 3D view using mol* of P16278-2 |
| 3D view using mol* of P16278-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of P16278-1 |
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| pLDDT distribution across the protein length of P16278-2 |
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| pLDDT distribution across the protein length of P16278-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of P16278-1 |
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| Ramachandran plot of P16278-3 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| P16278-1 | 1.025 | 108 | 1.024 | 469.567 | 0.638 | 0.736 | 0.951 | 0.356 | 1.095 | 0.326 | 0.754 | 58,59,60,61,88,91,92,101,102,130,312,313,314,315,3 16,317,392,393,394,395,410,411,412,413,414,513,514 ,515,516,517,518,521,585,586,587 |
| P16278-2 | 1.016 | 479 | 1.046 | 1535.268 | 0.591 | 0.7 | 0.885 | 0.49 | 0.965 | 0.508 | 0.728 | 56,58,59,83,85,86,87,88,89,90,91,107,108,109,110,1 11,112,115,119,120,123,124,137,139,141,142,143,144 ,145,146,147,148,149,150,151,153,175,182,185,186,1 87,188,190,192,193,194,195,196,200,202,276,281,282 ,310,311,323,325,326,327,328,348,349,350,351,352,3 53,354,415,446,461,463,464,465,466,491,515,516,517 ,519,529,530,531,532,533,534,535,536,537,538,539,5 40,541,542 |
| P16278-3 | 1.032 | 116 | 1.034 | 456.533 | 0.577 | 0.746 | 0.975 | 0.448 | 1.083 | 0.413 | 0.742 | 28,29,31,58,61,62,71,100,284,285,286,287,363,364,3 65,380,381,382,383,384,385,483,484,485,486,487,488 ,491,556,557 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of P16278-1_P16278-1_3thd_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P16278-1_3thd_A_P16278-2.pdb |
| 3D view using mol* of P16278-1_3thd_A_P16278-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P16278-1_P16278-2.pdb |
| 3D view using mol* of P16278-1_P16278-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P16278-1_vs_P16278-2.png |
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| ./stats/secondary_structure/figure/P16278-1_vs_P16278-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P16278-1_vs_P16278-2.png |
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| ./stats/relative_asa/P16278-1_vs_P16278-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to GLB1 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
| P16278 | GLB1 | DB04465 | Lactose | approved, experimental, investigational |
Related Diseases to GLB1 |
| Previous studies relating to the alternative splicing of GLB1 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| GLB1 | 2511208 | Alternative splicing of beta-galactosidase mRNA generates the classic lysosomal enzyme and a beta-galactosidase-related protein. | We have isolated two cDNAs encoding human lysosomal beta-galactosidase, the enzyme deficient in GM1-gangliosidosis and Morquio B syndrome, and a beta-galactosidase-related protein. In total RNA from normal fibroblasts a major mRNA of about 2.5 kilobases (kb) is recognized by cDNA probes. A minor transcript of about 2.0 kb is visible only in immunoselected polysomal RNA. A heterogeneous pattern of expression of the 2.5-kb beta-galactosidase transcript is observed in fibroblasts from different GM1-gangliosidosis patients. The nucleotide sequences of the two cDNAs are extensively colinear. However, the short cDNA misses two noncontiguous protein-encoding regions (1 and 2) present in the long cDNA. The exclusion of region 1 in the short molecule introduces a frameshift in its 3'-flanking sequence, which is restored by the exclusion of region 2. These findings imply the existence of two mRNA templates, which are read in a different frame only in the nucleotide stretch between regions 1 and 2. Sequence analysis of genomic exons of the beta-galactosidase gene shows that the short mRNA is generated by alternative splicing. The long and short cDNAs direct the synthesis in COS-1 cells of beta-galactosidase polypeptides of 85 and 68 kDa, respectively. Only the long protein is catalytically active under the assay conditions used, and it is capable of correcting beta-galactosidase activity after endocytosis by GM1-gangliosidosis fibroblasts. The subcellular localization of cDNA-encoded beta-galactosidase and beta-galactosidase-related proteins is different. | D005733 | Gangliosidoses |
Clinically important variants in GLB1 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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