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(-) Description

Title :  ORTHORHOMBIC CRYSTAL FORM OF BOGT6A E192Q IN COMPLEX WITH GALNAC
 
Authors :  T. Pham, B. Stinson, N. Thiyagarajan, M. Lizotte-Waniewski, K. Brew, K. R. Acharya
Date :  19 Dec 13  (Deposition) - 05 Feb 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. T. K. Pham, B. Stinson, N. Thiyagarajan, M. Lizotte-Waniewski, K. Brew, K. R. Acharya
Structures Of Complexes Of A Metal-Independent Glycosyltransferase Gt6 From Bacteroides Ovatus With Udp- Galnac And Its Hydrolysis Products.
J. Biol. Chem. V. 289 8041 2014
PubMed-ID: 24459149  |  Reference-DOI: 10.1074/JBC.M113.545384

(-) Compounds

Molecule 1 - GLYCOSYLTRANSFERASE FAMILY 6
    Atcc: 8483
    Chains: A, B, C, D
    EC Number: 2.4.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET42B
    Expression System Vector Type: PLASMID
    Fragment: ACTIVE SITE, RESIDUES 1-246
    Mutation: YES
    Organism Scientific: BACTEROIDES OVATUS
    Organism Taxid: 28116
    Synonym: GLYCOSYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1A2G4Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:95 , HIS A:122 , ALA A:155 , GLY A:157 , ASP A:191 , LEU A:213BINDING SITE FOR RESIDUE A2G A1237
2AC2SOFTWAREASN B:95 , GLY B:156 , TRP B:189 , ASP B:191 , GLN B:192BINDING SITE FOR RESIDUE A2G B1237
3AC3SOFTWAREASN C:95 , HIS C:122 , ALA C:155 , GLY C:156 , GLY C:157 , ASP C:191 , ILE C:228BINDING SITE FOR RESIDUE A2G C1238
4AC4SOFTWAREHIS D:122 , ALA D:155 , GLY D:156 , GLY D:157 , GLN D:192BINDING SITE FOR RESIDUE A2G D1236

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CJB)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Trp A:66 -Pro A:67
2Ile A:188 -Trp A:189
3Trp B:66 -Pro B:67
4Trp C:66 -Pro C:67
5Trp D:66 -Pro D:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CJB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CJB)

(-) Exons   (0, 0)

(no "Exon" information available for 4CJB)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:236
 aligned with A7LVT2_BACO1 | A7LVT2 from UniProtKB/TrEMBL  Length:263

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
         A7LVT2_BACO1     1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDESLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQY 236
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeee.............eeeee......hhhhhhhhhhhhhhhhhhhhhh.eeeee...eee....hhhhh.......eeee........hhhhh........................eeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eeehhhhhee..........eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjb A   1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDQSLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQY 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      


Chain B from PDB  Type:PROTEIN  Length:236
 aligned with A7LVT2_BACO1 | A7LVT2 from UniProtKB/TrEMBL  Length:263

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
         A7LVT2_BACO1     1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDESLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQY 236
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeee.............eeeee......hhhhhhhhhhhh.hhhhhhhhh.eeeee...eee....hhhhh.......eeeee.......hhhhh....................eeeeeeeeehhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...eeehhhhhee..........eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjb B   1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDQSLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQY 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      


Chain C from PDB  Type:PROTEIN  Length:237
 aligned with A7LVT2_BACO1 | A7LVT2 from UniProtKB/TrEMBL  Length:263

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         A7LVT2_BACO1     1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDESLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQYG 237
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeee.............eeeee......hhhhhhhhhhhh.hhhhhhhhh.eeeee...eee....hhhhh.......eeeee.......hhhhh....................eeeeeeeeehhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeehhhhhee..........eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjb C   1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDQSLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQYG 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       


Chain D from PDB  Type:PROTEIN  Length:235
 aligned with A7LVT2_BACO1 | A7LVT2 from UniProtKB/TrEMBL  Length:263

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
         A7LVT2_BACO1     1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDESLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQ 235
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhh.hhhhhhhhhhhhh......eeeeeeee.............eeeee......hhhhhhhhhhhhhhhhhhhhhh.eeeee...eee....hhhhh.......eeee........hhhhh........................eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...eeehhhhhee..........eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjb D   1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDQSLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQ 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4CJB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CJB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CJB)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A7LVT2_BACO1 | A7LVT2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016758    transferase activity, transferring hexosyl groups    Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0005975    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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  4cjb
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  2.4.1.40
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A7LVT2_BACO1 | A7LVT2: 4ayj 4ayl 4cj8 4cjc

(-) Related Entries Specified in the PDB File

4cj8 MONOCLINIC CRYSTAL FORM OF BOGT6A E192Q IN COMPLEX WITH UDP-GALNAC, UDP AND GALNAC
4cjc ORTHORHOMBIC CRYSTAL FORM OF BOGT6A E192Q IN COMPLEX WITH UDP-GALNAC, UDP, GALNAC