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(-) Description

Title :  CRYSTAL STRUCTURE OF DROSOPHILA BETA1,4-GALACTOSYLTRANSFERASE-7
 
Authors :  B. Ramakrishnan, P. K. Qasba
Date :  23 Feb 10  (Deposition) - 16 Mar 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Mn-Udp Complex, Glycosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Ramakrishnan, P. K. Qasba
Crystal Structure Of The Catalytic Domain Of Drosophila Beta1, 4-Galactosyltransferase-7.
J. Biol. Chem. V. 285 15619 2010
PubMed-ID: 20236943  |  Reference-DOI: 10.1074/JBC.M109.099564

(-) Compounds

Molecule 1 - BETA-4-GALACTOSYLTRANSFERASE 7
    ChainsA
    EC Number2.4.1.-, 2.4.1.133
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    Gene4-GALACTOSYLTRANSFERASE-7, BETA-4GALT7, BETA1, BETA4GALT7, BETA4GALT7-RA, DMEL_CG11780
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymFI08434P

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:7 , PRO A:82 , PHE A:83 , ARG A:84 , ARG A:86 , PHE A:121 , ASP A:145 , VAL A:146 , ASP A:147 , TYR A:177 , TRP A:207 , HIS A:241 , HIS A:243 , ARG A:250 , MPD A:313 , MN A:314 , HOH A:328 , HOH A:349 , HOH A:372 , HOH A:421BINDING SITE FOR RESIDUE UDP A 312
2AC2SOFTWAREHOH A:22 , ARG A:123 , TYR A:177 , PHE A:182 , TRP A:207 , GLY A:208 , GLU A:210 , ASP A:211 , UDP A:312 , HOH A:329 , HOH A:483 , HOH A:498BINDING SITE FOR RESIDUE MPD A 313
3AC3SOFTWAREASP A:147 , HIS A:241 , HIS A:243 , UDP A:312 , HOH A:386BINDING SITE FOR RESIDUE MN A 314

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:255 -A:310
2A:300 -A:308

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LW6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LW6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LW6)

(-) Exons   (0, 0)

(no "Exon" information available for 3LW6)

(-) Sequences/Alignments

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:241
 aligned with Q9VBZ9_DROME | Q9VBZ9 from UniProtKB/TrEMBL  Length:322

    Alignment length:241
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 
         Q9VBZ9_DROME    71 GASVHKMALLVPFRDRFEELLQFVPHMTAFLKRQGVAHHIFVLNQVDRFRFNRASLINVGFQFASDVYDYIAMHDVDLLPLNDNLLYEYPSSLGPLHIAGPKLHPKYHYDNFVGGILLVRREHFKQMNGMSNQYWGWGLEDDEFFVRIRDAGLQVTRPQNIKTGTNDTFSHIHNRYHRKRDTQKCFNQKEMTRKRDHKTGLDNVKYKILKVHEMLIDQVPVTILNILLDCDVNKTPWCDCS 311
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Glyco_transf_7N-3lw6A02 A:71-161                                                           --Glyco_transf_7C-3lw6A01 A:164-246                                                  ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhh.....eeeee...eee...............ee..................eeeeehhhhhhh...........hhhhhhhhhhhhh.................eee...............hhhhhhh......hhhhh.eeeeeeeeeee..eeeeeeeeee......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lw6 A  71 GASVHKMALLVPFRDRFEELLQFVPHMTAFLKRQGVAHHIFVLNQVDRFRFNRASLINVGFQFASDVYDYIAMHDVDLLPLNDNLLYEYPSSLGPLHIAGPKLHPKYHYDNFVGGILLVRREHFKQMNGMSNQYWGWGLEDDEFFVRIRDAGLQVTRPQNIKTGTNDTFSHIHNRYHRKRDTQKCFNQKEMTRKRDHKTGLDNVKYKILKVHEMLIDQVPVTILNILLDCDVNKTPWCDCS 311
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 

   Legend:   → Mismatch (orange background)
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  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 3LW6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LW6)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9VBZ9_DROME | Q9VBZ9)
molecular function
    GO:0008378    galactosyltransferase activity    Catalysis of the transfer of a galactosyl group to an acceptor molecule, typically another carbohydrate or a lipid.
    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:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0046525    xylosylprotein 4-beta-galactosyltransferase activity    Catalysis of the reaction: UDP-galactose + O-beta-D-xylosylprotein = UDP + 4-beta-D-galactosyl-O-beta-D-xylosylprotein.
biological process
    GO:0006491    N-glycan processing    The conversion of N-linked glycan (N = nitrogen) structures from the initially transferred oligosaccharide to a mature form, by the actions of glycosidases and glycosyltransferases. The early processing steps are conserved and play roles in glycoprotein folding and trafficking.
    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.
    GO:0030206    chondroitin sulfate biosynthetic process    The chemical reactions and pathways resulting in the formation of chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.
    GO:0006024    glycosaminoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
    GO:0015012    heparan sulfate proteoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues; the former are a mixture of sulfated and nonsulfated D-glucuronic acid and L-iduronic acid; the L-iduronic acid is either sulfated or acetylated on its amino group as well as being sulfated on one of its hydroxyl groups; heparan sulfate chains are covalently linked to peptidyl-serine by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylosyl to serine residues.
    GO:0030166    proteoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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 Specified in the PDB File

1o0r CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF BETA1,4- GALACTOSYLTRANSFERASE-1