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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GLCAT-S APO FORM
 
Authors :  T. Shiba, S. Kakuda, M. Ishiguro, S. Oka, T. Kawasaki, S. Wakatsuki, R. Kato
Date :  03 Aug 05  (Deposition) - 18 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rossmann-Like Fold, Glucuronyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Shiba, S. Kakuda, M. Ishiguro, I. Morita, S. Oka, T. Kawasaki, S. Wakatsuki, R. Kato
Crystal Structure Of Glcat-S, A Human Glucuronyltransferase, Involved In The Biosynthesis Of The Hnk-1 Carbohydrate Epitope
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GALACTOSYLGALACTOSYLXYLOSYLPROTEIN 3-BETA- GLUCURONOSYLTRANSFERASE 2
    Chains: A, B, C, D
    EC Number: 2.4.1.135
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A(+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-1,3-GLUCURONYLTRANSFERASE 2, GLUCURONOSYLTRANSFERASE-S, GLCAT-S, UDP- GLUCURONOSYLTRANSFERASE-S, GLCAT-D

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2D0J)

(-) Sites  (0, 0)

(no "Site" information available for 2D0J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D0J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D0J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D0J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D0J)

(-) Exons   (4, 16)

Asymmetric Unit (4, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002300531ENSE00001150538chr6:71666741-716655421200B3GA2_HUMAN1-1971974A:78-197 (gaps)
B:78-197 (gaps)
C:78-197 (gaps)
D:79-197 (gaps)		120
120
120
119
1.2ENST000002300532ENSE00000758545chr6:71603975-71603831145B3GA2_HUMAN198-246494A:198-246
B:198-246
C:198-246
D:198-246		49
49
49
49
1.3ENST000002300533ENSE00000758544chr6:71571681-71571533149B3GA2_HUMAN246-295504A:246-295
B:246-295
C:246-295
D:246-295		50
50
50
50
1.4ENST000002300534ENSE00001150532chr6:71571452-715663825071B3GA2_HUMAN296-323284A:296-323
B:296-323
C:296-323
D:296-323		28
28
28
28

(-) 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:242
 aligned with B3GA2_HUMAN | Q9NPZ5 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:246
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
          B3GA2_HUMAN    78 QLPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPSTHLHVPTPRRYKRPGLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQEMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILSNPKAVFKRRGSQPGMQESDFLKQITTVEELEPKANNCTKVLVWHTRTEKVNLANEPKYHLDTVKIEV 323
               SCOP domains d2d0ja_ A: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains 2d0jA00 A:78-323 Spore Coat Polysaccharide Biosynthesis Protein SpsA;     Chain A                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh...eeeee......----....hhhhhhhhhhhhhhhh........eeee.....ee.hhhhhhhh....eee..eeee..eeeeeeeee..eeeeee...........hhh.eeeehhhhhhh..........hhhhhhhhhhhh..hhhhheehhhhhh...ee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:78-197 (gaps) UniProt: 1-197 [INCOMPLETE]                                                              Exon 1.2  PDB: A:198-246 UniProt: 198-246        -------------------------------------------------Exon 1.4  PDB: A:296-323     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:246-295 UniProt: 246-295         ---------------------------- Transcript 1 (2)
                 2d0j A  78 QLPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPSTHLHVPTPRR----GLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQEMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILSNPKAVFKRRGSQPGMQESDFLKQITTVEELEPKANNCTKVLVWHTRTEKVNLANEPKYHLDTVKIEV 323
                                    87        97       107       117       127       137       147    |  157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
                                                                                               147  152                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with B3GA2_HUMAN | Q9NPZ5 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:246
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
          B3GA2_HUMAN    78 QLPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPSTHLHVPTPRRYKRPGLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQEMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILSNPKAVFKRRGSQPGMQESDFLKQITTVEELEPKANNCTKVLVWHTRTEKVNLANEPKYHLDTVKIEV 323
               SCOP domains d2d0jb_ B: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains 2d0jB00 B:78-323 Spore Coat Polysaccharide Biosynthesis Protein SpsA;     Chain A                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh....eeeee......----....hhhhhhhhhhhhhhhh.......eeeee.....ee.hhhhhhhhh...eee..ee......eeeeeee..eeeeee...........hhh.eeeehhhhhhh.............hhhhhhhhh..hhhhheehhhhhh...ee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:78-197 (gaps) UniProt: 1-197 [INCOMPLETE]                                                              Exon 1.2  PDB: B:198-246 UniProt: 198-246        -------------------------------------------------Exon 1.4  PDB: B:296-323     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: B:246-295 UniProt: 246-295         ---------------------------- Transcript 1 (2)
                 2d0j B  78 QLPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPSTHLHVPTPRR----GLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQEMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILSNPKAVFKRRGSQPGMQESDFLKQITTVEELEPKANNCTKVLVWHTRTEKVNLANEPKYHLDTVKIEV 323
                                    87        97       107       117       127       137       147    |  157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
                                                                                               147  152                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:242
 aligned with B3GA2_HUMAN | Q9NPZ5 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:246
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
          B3GA2_HUMAN    78 QLPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPSTHLHVPTPRRYKRPGLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQEMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILSNPKAVFKRRGSQPGMQESDFLKQITTVEELEPKANNCTKVLVWHTRTEKVNLANEPKYHLDTVKIEV 323
               SCOP domains d2d0jc_ C: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains 2d0jC00 C:78-323 Spore Coat Polysaccharide Biosynthesis Protein SpsA;     Chain A                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh..eeeee......----....hhhhhhhhhhhhhhhh.......eeeee.....ee.hhhhhhhh....eee..eeee..eeeeeeeee..eeeeee...........hhh.eeeehhhhhhh.............hhhhhhhhh..hhhhheehhhhhh...ee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: C:78-197 (gaps) UniProt: 1-197 [INCOMPLETE]                                                              Exon 1.2  PDB: C:198-246 UniProt: 198-246        -------------------------------------------------Exon 1.4  PDB: C:296-323     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: C:246-295 UniProt: 246-295         ---------------------------- Transcript 1 (2)
                 2d0j C  78 QLPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPSTHLHVPTPRR----GLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQEMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILSNPKAVFKRRGSQPGMQESDFLKQITTVEELEPKANNCTKVLVWHTRTEKVNLANEPKYHLDTVKIEV 323
                                    87        97       107       117       127       137       147    |  157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
                                                                                               147  152                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:241
 aligned with B3GA2_HUMAN | Q9NPZ5 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:245
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318     
          B3GA2_HUMAN    79 LPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPSTHLHVPTPRRYKRPGLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQEMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILSNPKAVFKRRGSQPGMQESDFLKQITTVEELEPKANNCTKVLVWHTRTEKVNLANEPKYHLDTVKIEV 323
               SCOP domains d2d0jd_ D: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains 2d0jD00 D:79-323 Spore Coat Polysaccharide Biosynthesis Protein SpsA;     Chain A                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh..eeeee......----....hhhhhhhhhhhhhhhh........eeee.....ee.hhhhhhhhh...eee..eeee..eeeeeeee....eeeee...........hhh.eeeehhhhhhh.............hhhhhhhhhhhhhhhheehhhhhh...ee........................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: D:79-197 (gaps) UniProt: 1-197 [INCOMPLETE]                                                             Exon 1.2  PDB: D:198-246 UniProt: 198-246        -------------------------------------------------Exon 1.4  PDB: D:296-323     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: D:246-295 UniProt: 246-295         ---------------------------- Transcript 1 (2)
                 2d0j D  79 LPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPSTHLHVPTPRR----GLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQEMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILSNPKAVFKRRGSQPGMQESDFLKQITTVEELEPKANNCTKVLVWHTRTEKVNLANEPKYHLDTVKIEV 323
                                    88        98       108       118       128       138        |-   |   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318     
                                                                                              147  152
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D0J)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (B3GA2_HUMAN | Q9NPZ5)
molecular function
    GO:0015018    galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity    Catalysis of the reaction: UDP-glucuronate + 3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein = UDP + 3-beta-D-glucuronosyl-3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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.
    GO:0030204    chondroitin sulfate metabolic process    The chemical reactions and pathways involving 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. They usually occur linked to a protein to form proteoglycans. Two subgroups exist, one in which the sulfate is on the 4-position (chondroitin sulfate A) and the second in which it is in the 6-position (chondroitin sulfate C). They often are polydisperse and often differ in the degree of sulfation from tissue to tissue. The chains of repeating disaccharide are covalently linked to the side chains of serine residues in the polypeptide backbone of a protein by a glycosidic attachment through the trisaccharide unit galactosyl-galactosyl-xylosyl. Chondroitin sulfate B is more usually known as dermatan sulfate.
    GO:0050650    chondroitin sulfate proteoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of chondroitin sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Chondroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues; the repeat units consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.
    GO:0030203    glycosaminoglycan metabolic process    The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties.
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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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