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Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-GalNAc derived inhibitor (3GW and 4GW)
Biology and Chemistry Report
3V0N
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/TRANSFERASE INHIBITOR
    Text GTA, ABO, CISAB MUTANT, ROSSMANN FOLD, "closed" CONFORMATION, GLYCOSYLTRANSFERASE, GLYCOPROTEIN, BLOOD GROUP ANTIGEN, UDP-GalNAc, METAL-BINDING, MANGANESE, Glycosylation, TRANSMEMBRANE, GOLGI APPARATUS, SECRETED, SIGNAL-ANCHOR, TRANSFERASE-TRANSFERASE INHIBITOR complex

    Polymeric Molecules

    Chain A,B
    Description Histo-blood group ABO system transferase 
    Fragment Extracellular catalytic domain 
    Mutation L266G, G268A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 34654.3 
    Source Method genetically manipulated  
    Entity Name Fucosylglycoprotein 3-alpha-galactosyltransferase, Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase, Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, Glycoprotein-fucosylgalactoside alpha-galactosyltransferase, Histo-blood group A transferase, A transferase, Histo-blood group B transferase, B transferase, NAGAT, Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    3GW  5-(5-formylthiophen-2-yl)uridine-5'(2-(acetylamino)-2-deoxy-alpha-D-galactosyl)-diphosphate  C22 H29 N3 O18 P2 S   717.49  View 
    4GW  5-(5-formylthiophen-2-yl)uridine 5'-(trihydrogen diphosphate)  C14 H16 N2 O13 P2 S   514.30  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    MN  MANGANESE (II) ION  Mn   54.94  View 
    SO4  SULFATE ION  O4 S   96.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B BGAT_HUMAN P16442     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  2.4.1.37      
    A B  2.4.1.40      
    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. 
    16020   Membrane  A Lipid Bilayer Along with All the Proteins and Protein Complexes Embedded in It an Attached to It. 
    16758   Transferase Activity Transferring Hexosyl Groups  Catalysis of the Transfer of a Hexosyl Group From One Compound (donor) to Another (acceptor). 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ab0, abo
    Host Scientific Name Escherichia coli  
    Host Strain Bl21
    Host Vector Type Plasmid
    Host Plasmid Name PCW DELTA 1AC


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    9 9q34.2 28     ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1 ABO    

    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
    rs549446 LS-SNP   dbSNP   A 63 R - > HL Coil 23% (Intermediate) 9 136135238
    rs56335272 LS-SNP   dbSNP   A 64 V - > I Coil 20% (Intermediate) 9 136135236
    rs55958637 LS-SNP   dbSNP   A 68 R - > T Coil 48% (Exposed) 9 136135223
    rs55742010 LS-SNP   dbSNP   A 83 D - > Y Bend 40% (Exposed) 9 136132922
    rs77641731 LS-SNP   dbSNP   A 88 T - > A Coil 0% (Buried) 9 136132908
    rs56072655 LS-SNP   dbSNP   A 100 F - > IV Coil 13% (Intermediate) 9 136132872
    rs181412963 LS-SNP   dbSNP   A 106 N - > S Helix 29% (Intermediate) 9 136132853
    rs56188150 LS-SNP   dbSNP   A 107 E - > *Q Helix 36% (Intermediate) 9 136132851
    rs55718818 LS-SNP   dbSNP   A 108 Q - > LP Helix 16% (Intermediate) 9 136132847
    rs56390827 LS-SNP   dbSNP   A 110 R - > K Helix 44% (Exposed) 9 136132841
    rs55770802 LS-SNP   dbSNP   A 118 L - > IV Beta Ladder 1% (Buried) 9 136132818
    rs55658842 LS-SNP   dbSNP   A 136 T - > M Helix 10% (Intermediate) 9 136131711
    rs55687353 LS-SNP   dbSNP   A 152 F - > L Beta Ladder 0% (Buried) 9 136131664
    rs1053878 LS-SNP   dbSNP   A 156 P - > L 3/10 Helix 38% (Exposed) 9 136131651
    rs8176738 LS-SNP   dbSNP   A 161 R - > H Coil 97% (Exposed) 9 136131636
    rs55756402 LS-SNP   dbSNP   A 163 T - > M Coil 94% (Exposed) 9 136131630
    rs56043861 LS-SNP   dbSNP   A 168 R - > GW Beta Ladder 10% (Intermediate) 9 136131616
    rs7853989 LS-SNP   dbSNP   A 176 R - > G Coil 61% (Exposed) 9 136131592
    rs56039827 LS-SNP   dbSNP   A 176 R - > H Coil 61% (Exposed) 9 136131591
    rs55687199 LS-SNP   dbSNP   A 177 A - > T Coil 33% (Intermediate) 9 136131589
    rs56258249 LS-SNP   dbSNP   A 180 R - > HP Bend 38% (Exposed) 9 136131579
    rs56164697 LS-SNP   dbSNP   A 180 R - > C Bend 38% (Exposed) 9 136131580
    rs56044929 LS-SNP   dbSNP   A 183 D - > N Helix 17% (Intermediate) 9 136131571
    rs56089890 LS-SNP   dbSNP   A 183 D - > G Helix 17% (Intermediate) 9 136131570
    rs56189011 LS-SNP   dbSNP   A 186 M - > V Helix 9% (Buried) 9 136131562
    rs56234761 LS-SNP   dbSNP   A 187 R - > H Helix 15% (Intermediate) 9 136131558
    rs184446112 LS-SNP   dbSNP   A 188 R - > S Helix 12% (Intermediate) 9 136131556 NULL
    rs56223957 LS-SNP   dbSNP   A 198 R - > W Helix 69% (Exposed) 9 136131526
    rs8176739 LS-SNP   dbSNP   A 199 R - > C Turn 27% (Intermediate) 9 136131523
    rs181536132 LS-SNP   dbSNP   A 210 V - > M Beta Ladder 3% (Buried) 9 136131490 NULL
    rs55827808 LS-SNP   dbSNP   A 214 M - > R Beta Ladder 4% (Buried) 9 136131477 NULL
    rs55900544 LS-SNP   dbSNP   A 216 F - > Y Beta Ladder 2% (Buried) 9 136131471
    rs8176740 LS-SNP   dbSNP   A 216 F - > I Beta Ladder 2% (Buried) 9 136131472
    rs56408700 LS-SNP   dbSNP   A 217 R - > C Coil 34% (Intermediate) 9 136131469
    rs56031507 LS-SNP   dbSNP   A 222 V - > M 3/10 Helix 0% (Buried) 9 136131454
    rs56159791 LS-SNP   dbSNP   A 223 E - > D 3/10 Helix 0% (Buried) 9 136131449
    rs56116432 LS-SNP   dbSNP   A 230 G - > D Beta Ladder 0% (Buried) 9 136131429
    rs55739900 LS-SNP   dbSNP   A 232 L - > P Beta 1% (Buried) 9 136131423
    rs56287010 LS-SNP   dbSNP   A 233 H - > Q Coil 24% (Intermediate) 9 136131419
    rs55722397 LS-SNP   dbSNP   A 234 P - > AS Turn 10% (Intermediate) 9 136131418
    rs8176743 LS-SNP   dbSNP   A 235 G - > S Turn 42% (Exposed) 9 136131415
    rs55951833 LS-SNP   dbSNP   A 241 R - > W Turn 12% (Intermediate) 9 136131397
    rs55752071 LS-SNP   dbSNP   A 251 Q - > P Turn 66% (Exposed) 9 136131366
    rs56222087 LS-SNP   dbSNP   A 252 S - > A Bend 2% (Buried) 9 136131364
    rs56327413 LS-SNP   dbSNP   A 254 A - > V Turn 1% (Buried) 9 136131357
    rs55751228 LS-SNP   dbSNP   A 256 I - > T Coil 0% (Buried) 9 136131351
    rs56396277 LS-SNP   dbSNP   A 259 D - > G Turn 39% (Exposed) 9 136131342
    rs56323007 LS-SNP   dbSNP   A 260 E - > K Coil 6% (Buried) 9 136131340
    rs56277033 LS-SNP   dbSNP   A 262 D - > N Bend 1% (Buried) 9 136131334
    rs8176746 LS-SNP   dbSNP   A 266 L - > M Coil 0% (Buried) 9 136131322
    rs55797499 LS-SNP   dbSNP   A 267 G - > E Turn 4% (Buried) 9 136131318
    rs8176747 LS-SNP   dbSNP   A 268 G - > A Turn 11% (Intermediate) 9 136131315
    rs41302905 LS-SNP   dbSNP   A 268 G - > R Turn 11% (Intermediate) 9 136131316
    rs8176748 LS-SNP   dbSNP   A 277 V - > M Helix 0% (Buried) 9 136131289
    rs56106480 LS-SNP   dbSNP   A 280 L - > F Helix 0% (Buried) 9 136131280
    rs34163698 LS-SNP   dbSNP   A 283 A - > V Helix 30% (Intermediate) 9 136131270
    rs55805279 LS-SNP   dbSNP   A 288 M - > R Helix 5% (Buried) 9 136131255
    rs56355240 LS-SNP   dbSNP   A 291 D - > E Helix 1% (Buried) 9 136131245
    rs56409303 LS-SNP   dbSNP   A 291 D - > N Helix 1% (Buried) 9 136131247
    rs55783488 LS-SNP   dbSNP   A 298 A - > V Coil 1% (Buried) 9 136131225
    rs55699308 LS-SNP   dbSNP   A 306 L - > R Helix 0% (Buried) 9 136131201
    rs56346931 LS-SNP   dbSNP   A 309 Y - > C Helix 7% (Buried) 9 136131192
    rs55927860 LS-SNP   dbSNP   A 322 E - > G 3/10 Helix 0% (Buried) 9 136131153
    rs55904390 LS-SNP   dbSNP   A 324 L - > W Bend 7% (Buried) 9 136131147
    rs56231718 LS-SNP   dbSNP   A 337 R - > G Bend 48% (Exposed) 9 136131109