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An Information Portal to 105025 Biological Macromolecular Structures

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate
Biology and Chemistry Report
3IGU
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text GLYCOPROTEIN, CARBOHYDRATE-BINDING PROTEIN, GLYCOSIDASE, LYSOSOMAL ENZYME, (BETA/ALPHA)8 BARREL, Schindler disease, Kanzaki disease, Disease mutation, Disulfide bond, Epilepsy, Hydrolase, Lysosome, Phosphoprotein

    Polymeric Molecules

    Chain A,B
    Description Alpha-N-acetylgalactosaminidase 
    Mutation N201Q 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 45583.3 
    Source Method genetically manipulated  
    Entity Name Alpha-galactosidase B 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    7JZ  2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose  C6 H10 F2 O5   200.14  View 
    BMA  BETA-D-MANNOSE  C6 H12 O6   180.16  View 
    FUC  ALPHA-L-FUCOSE  C6 H12 O5   164.16  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    MAN  ALPHA-D-MANNOSE  C6 H12 O6   180.16  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B NAGAB_HUMAN P17050     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    A B  3.2.1.49        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    5975   Carbohydrate Metabolic Process  The Chemical Reactions and Pathways Involving Carbohydrates Any of a Group of Organic Compounds Based of the General Formula Cx(h2o)y. Includes the Formation of Carbohydrate Derivatives by the Addition of a Carbohydrate Residue to Another Molecule. 
    8152   Metabolic Process  The Chemical Reactions and Pathways Including Anabolism and Catabolism by Which Living Organisms Transform Chemical Substances. Metabolic Processes Typically Transform Small Molecules But Also Include Macromolecular Processes Such As DNA Repair and Replication and Protein Synthesis and Degradation. 
    9311   Oligosaccharide Metabolic Process  The Chemical Reactions and Pathways Involving Oligosaccharides Molecules with Between Two and (about) 20 Monosaccharide Residues Connected by Glycosidic Linkages. 
    16052   Carbohydrate Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Carbohydrates Any of a Group of Organic Compounds Based of the General Formula Cx(h2o)y. 
    16139   Glycoside Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Glycosides Compounds in Which a Glycosyl Group Is Substituted Into a Hydroxyl Thiol or Selenol Group in Another Compound. 
    19377   Glycolipid Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Glycolipid a Class of 1 2 Di O Acylglycerols Joined At Oxygen 3 by a Glycosidic Linkage to a Carbohydrate Part (usually a Mono Di or Tri Saccharide). 
    46477   Glycosylceramide Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Glycosylceramides Any Compound Formed by the Replacement of the Glycosidic Hydroxyl Group of a Cyclic Form of a Monosaccharide (or Derivative) by a Ceramide Group. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5764   Lysosome  A Small Lytic Vacuole That Has Cell Cycle Independent Morphology and Is Found in Most Animal Cells and That Contains a Variety of Hydrolases Most of Which Have Their Maximal Activities in the Ph Range 5 6. the Contained Enzymes Display Latency If Properly Isolated. About 40 Different Lysosomal Hydrolases Are Known and Lysosomes Have a Great Variety of Morphologies and Functions. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    4553   Hydrolase Activity Hydrolyzing O Glycosyl Compounds  Catalysis of the Hydrolysis of Any O Glycosyl Bond. 
    4557   Alpha Galactosidase Activity  Catalysis of the Hydrolysis of Terminal Non Reducing Alpha D Galactose Residues in Alpha D Galactosides Including Galactose Oligosaccharides Galactomannans and Galactohydrolase. 
    8456   Alpha N Acetylgalactosaminidase Activity  Catalysis of the Hydrolysis of Terminal Non Reducing N Acetyl D Galactosamine Residues in N Acetyl Alpha D Galactosaminides. 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    16798   Hydrolase Activity Acting On Glycosyl Bonds  Catalysis of the Hydrolysis of Any Glycosyl Bond. 
    42803   Protein Homodimerization Activity  Interacting Selectively and Non Covalently with an Identical Protein to Form a Homodimer. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Details Selected with Blastocidin
    Gene naga
    Host Scientific Name Trichoplusia ni  
    Host Strain Hi Five
    Host Vector Type Stable Cell Line
    Host Plasmid Name pIB/V5-His-TOPO TA


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    22 22q11 4668     N-acetylgalactosaminidase, alpha- NAGA    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs199834981 LS-SNP   dbSNP   A 37 R - > H Turn 10% (Intermediate) 22 42464485
    rs201553220 LS-SNP   dbSNP   A 66 G - > R Bend 20% (Intermediate) 22 42463897
    rs202010344 LS-SNP   dbSNP   A 83 G - > S Beta Ladder 44% (Exposed) 22 42463846
    rs73167107 LS-SNP   dbSNP   A 94 D - > N Coil 19% (Intermediate) 22 42463813
    rs140775168 LS-SNP   dbSNP   A 97 R - > G Turn 6% (Buried) 22 42463804
    rs147270239 LS-SNP   dbSNP   A 101 G - > D Coil 20% (Intermediate) 22 42463791
    rs3747186 LS-SNP   dbSNP   A 118 I - > V Beta Ladder 1% (Buried) 22 42463267
    rs186173534 LS-SNP   dbSNP   A 136 D - > N 3/10 Helix 77% (Exposed) 22 42463213
    rs113848447 LS-SNP   dbSNP   A 142 A - > T Helix 0% (Buried) 22 42463195
    rs201086964 LS-SNP   dbSNP   A 142 A - > V Helix 0% (Buried) 22 42463194
    rs138260186 LS-SNP   dbSNP   A 143 Q - > H Helix 49% (Exposed) 22 42463190
    rs200580292 LS-SNP   dbSNP   A 152 M - > V Beta Ladder 2% (Buried) 22 42463165
    rs121434532 LS-SNP   dbSNP   A 160 S - > C Coil 17% (Intermediate) 22 42463140 NAG
    rs141557187 LS-SNP   dbSNP   A 161 T - > I Coil 37% (Exposed) 22 42463137 NAG
    rs200080569 LS-SNP   dbSNP   A 165 R - > W Helix 7% (Buried) 22 42463126
    rs139027070 LS-SNP   dbSNP   A 198 P - > T Turn 91% (Exposed) 22 42462719
    rs201294991 LS-SNP   dbSNP   A 233 V - > M Helix 6% (Buried) 22 42461804
    rs145191031 LS-SNP   dbSNP   A 238 I - > V Helix 43% (Exposed) 22 42461789
    rs202212429 LS-SNP   dbSNP   A 256 I - > T Turn 1% (Buried) 22 42459021
    rs140238609 LS-SNP   dbSNP   A 263 L - > I Helix 34% (Intermediate) 22 42459001
    rs138546784 LS-SNP   dbSNP   A 267 R - > G Helix 29% (Intermediate) 22 42458989
    rs144669656 LS-SNP   dbSNP   A 273 W - > C Helix 0% (Buried) 22 42458969
    rs201208218 LS-SNP   dbSNP   A 282 M - > I Beta Ladder 1% (Buried) 22 42458942
    rs121434529 LS-SNP   dbSNP   A 325 E - > K Beta Ladder 5% (Buried) 22 42457056
    rs140356002 LS-SNP   dbSNP   A 328 M - > T Beta Ladder 20% (Intermediate) 22 42457046
    rs121434530 LS-SNP   dbSNP   A 329 R - > W Beta Ladder 0% (Buried) 22 42457044
    rs121434533 LS-SNP   dbSNP   A 329 R - > Q Beta Ladder 0% (Buried) 22 42457043
    rs144560510 LS-SNP   dbSNP   A 337 A - > T Beta Ladder 0% (Buried) 22 42457020
    rs140711222 LS-SNP   dbSNP   A 347 M - > T Bend 19% (Intermediate) 22 42456989
    rs147253075 LS-SNP   dbSNP   A 362 G - > W Bend 38% (Exposed) 22 42456945
    rs199980021 LS-SNP   dbSNP   A 362 G - > V Bend 38% (Exposed) 22 42456944
    rs142863015 LS-SNP   dbSNP   A 367 E - > K Beta Ladder 20% (Intermediate) 22 42456930
    rs148538178 LS-SNP   dbSNP   A 379 G - > S Beta Ladder 44% (Exposed) 22 42456384
    rs144771084 LS-SNP   dbSNP   A 381 R - > Q Coil 51% (Exposed) 22 42456377