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(-) Description

Title :  ORTHORHOMBIC CRYSTAL FORM OF BOGT6A E192Q IN COMPLEX WITH UDP-GALNAC, UDP, 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 :  3.42
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, Orthorhombic Form, Metal-Independent, Hydrolysed Products (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
    Atcc8483
    ChainsA, B, C, D
    EC Number2.4.1.40
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET42B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentACTIVE SITE, RESIDUES 1-246
    MutationYES
    Organism ScientificBACTEROIDES OVATUS
    Organism Taxid28116
    SynonymGLYCOSYLTRANSFERASE

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2UD22Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1A2G-1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2UD21Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
3UDP-1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2UD2-1Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1A2G-1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2UD21Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
3UDP-1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2UD2-1Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:8 , THR A:10 , TYR A:13 , TRP A:66 , ASN A:69 , THR A:70 , ARG A:73 , ASN A:95 , ALA A:96 , HIS A:122 , GLY A:156 , ASP A:191 , GLN A:192 , LYS A:231BINDING SITE FOR RESIDUE UD2 A1242
2AC2SOFTWAREILE C:8 , THR C:10 , TYR C:13 , TRP C:66 , ASN C:69 , THR C:70 , ARG C:73 , ASN C:95 , ALA C:96 , HIS C:122 , ALA C:155 , GLY C:156 , GLY C:157 , TRP C:189 , HIS C:190 , ASP C:191 , GLN C:192 , LYS C:231BINDING SITE FOR RESIDUE UD2 C1241
3AC3SOFTWARETHR B:10 , TYR B:13 , ASN B:63 , ASN B:69 , THR B:70 , ASN B:95 , ALA B:96 , LYS B:231 , HIS D:184BINDING SITE FOR RESIDUE UDP B1239
4AC4SOFTWAREILE D:8 , CYS D:9 , THR D:10 , TYR D:13 , ASN D:69 , THR D:70 , ALA D:96 , LYS D:231BINDING SITE FOR RESIDUE UDP D1237
5AC5SOFTWAREGLN B:192BINDING SITE FOR RESIDUE A2G B1240
6AC6SOFTWAREHIS D:122 , THR D:134 , GLN D:192BINDING SITE FOR RESIDUE A2G D1238

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Tyr A:48 -Asp A:49
2Trp A:66 -Pro A:67
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 4CJC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CJC)

(-) 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:241
 aligned with A7LVT2_BACO1 | A7LVT2 from UniProtKB/TrEMBL  Length:263

    Alignment length:241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
         A7LVT2_BACO1     1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDESLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQYGGHEL 241
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhh......eeeeeeee..............eeee......hhhhhhhhhhhhh..hhhhhh..eeeee...eee....hhhhh.......eeee........hhhhh........................eeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eeehhhhhee..........eee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjc A   1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDQSLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQYGGHEL 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with A7LVT2_BACO1 | A7LVT2 from UniProtKB/TrEMBL  Length:263

    Alignment length:238
                                    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 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDESLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQYGG 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhh......eeeeeeee.............eeeee......hhhhhhhhhhh....hhhhhh..eeeee...eee....hhhhh.......eeeee.......hhhhh....................eeeeeeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eeehhhhhee..........eee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjc B   1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDQSLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQYGG 238
                                    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:240
 aligned with A7LVT2_BACO1 | A7LVT2 from UniProtKB/TrEMBL  Length:263

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
         A7LVT2_BACO1     1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDESLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQYGGHE 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhhh......eeeeeeee..............eeee......hhhhhhhhhhhhh..hhhhhhh.eeeee...eee....hhhhh.......eeeee.......hhhhh....................eeeeeeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eeehhhhhee..........eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cjc C   1 MRIGILYICTGKYDIFWKDFYLSAERYFMQDQSFIIEYYVFTDSPKLYDEENNKHIHRIKQKNLGWPDNTLKRFHIFLRIKEQLERETDYLFFFNANLLFTSPIGKEILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYIPEGEGRYYYAGGLSGGCTKAYLKLCTTICSWVDRDATNHIIPIWHDQSLINKYFLDNPPAITLSPAYLYPEGWLLPFEPIILIRDKNKPQYGGHE 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain D 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 .eeeeeeee..hhhhhhhhhhhhhhhh.......eeeeeeee........................hhhhhhhhhhh..hhhhhhh...eeeee...eee....hhhhh.......ee..........hhhhh........................eeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhee..........eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjc D   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      

   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 4CJC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        A7LVT2_BACO1 | A7LVT24ayj 4ayl 4cj8 4cjb

(-) Related Entries Specified in the PDB File

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