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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GLCAT-P IN COMPLEX WITH UDP AND MN2+
 
Authors :  S. Kakuda, T. Shiba, M. Ishiguro, H. Tagawa, S. Oka, Y. Kajihara, T. Kawasaki, S. Wakatsuki, R. Kato
Date :  27 Dec 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Glycoprotein, Glycocyltransferase, Hnk-1 Epitope (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kakuda, T. Shiba, M. Ishiguro, H. Tagawa, S. Oka, Y. Kajihara, T. Kawasaki, S. Wakatsuki, R. Kato
Structural Basis For Acceptor Substrate Recognition Of A Human Glucuronyltransferase, Glcat-P, An Enzyme Critical In The Biosynthesis Of The Carbohydrate Epitope Hnk-1
J. Biol. Chem. V. 279 22693 2004
PubMed-ID: 14993226  |  Reference-DOI: 10.1074/JBC.M400622200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GALACTOSYLGALACTOSYLXYLOSYLPROTEIN 3-BETA- GLUCURONOSYLTRANSFERASE 1
    Chains: A, B
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2TLA1Ligand/IonL(+)-TARTARIC ACID
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:197 , UDP A:503 , HOH A:504 , HOH A:505BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWAREASP B:197 , UDP B:504 , HOH B:505 , HOH B:506BINDING SITE FOR RESIDUE MN B 502
3AC3SOFTWAREARG A:231 , ARG A:240 , TRP A:241 , HIS A:248 , HOH A:618 , HOH A:636 , ARG B:213 , ARG B:263 , GLN B:267BINDING SITE FOR RESIDUE TLA A 500
4AC4SOFTWAREPRO A:91 , THR A:92 , TYR A:93 , ASP A:122 , LYS A:153 , ARG A:165 , GLY A:166 , ARG A:170 , ASP A:195 , ASP A:196 , ASP A:197 , HIS A:311 , ARG A:313 , MN A:501 , HOH A:584BINDING SITE FOR RESIDUE UDP A 503
5AC5SOFTWAREPRO B:91 , THR B:92 , TYR B:93 , ASP B:122 , ARG B:165 , GLY B:166 , ASP B:195 , ASP B:196 , ASP B:197 , HIS B:311 , ARG B:313 , MN B:502 , HOH B:591 , HOH B:611 , HOH B:681 , HOH B:725BINDING SITE FOR RESIDUE UDP B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V83)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V83)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_044538A131TB3GA1_HUMANPolymorphism35434644A/BA131T
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V83)

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003925801ENSE00000999945chr11:134281812-134281701112B3GA1_HUMAN-00--
1.3bENST000003925803bENSE00001512424chr11:134257834-134257721114B3GA1_HUMAN-00--
1.3dENST000003925803dENSE00001512423chr11:134257588-134257442147B3GA1_HUMAN1-38380--
1.4cENST000003925804cENSE00000749062chr11:134254082-134253574509B3GA1_HUMAN38-2071702A:83-207 (gaps)
B:82-207 (gaps)		125
126
1.5ENST000003925805ENSE00000749063chr11:134252900-134252604297B3GA1_HUMAN208-306992A:208-306
B:208-306		99
99
1.6ENST000003925806ENSE00000800138chr11:134251918-134251818101B3GA1_HUMAN307-334282A:307-334
B:307-334		28
28
1.8bENST000003925808bENSE00001387274chr11:134250641-1342484002242B3GA1_HUMAN-00--

(-) 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
(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:245
 aligned with B3GA1_HUMAN | Q9P2W7 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:252
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332  
          B3GA1_HUMAN    83 LPTIHVVTPTYSRPVQKAELTRMANTLLHVPNLHWLVVEDAPRRTPLTARLLRDTGLNYTHLHVETPRNYKLRGDARDPRIPRGTMQRNLALRWLRETFPRNSSQPGVVYFADDDNTYSLELFEEMRSTRRVSVWPVAFVGGLRYEAPRVNGAGKVVGWKTVFDPHRPFAIDMAGFAVNLRLILQRSQAYFKLRGVKGGYQESSLLRELVTLNDLEPKAANCTKILVWHTRTEKPVLVNEGKKGFTDPSVEI 334
               SCOP domains d1v83a_ A: Beta-1,3-glucuronyltransferase 1, GlcAT-P                                                                                                                                                                                                         SCOP domains
               CATH domains 1v83A00 A:83-334 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Ch       ain A                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh.eeeeee...hhhhhh-------....hhhhhhhhhhhhhhhh.......eeeee.....eehhhhhhhhhh...eee..ee......eeeeee.....eeeee...........hhh.eeeehhhhhhh.............hhhhhhhh...hhh.eeehhhhhh...ee........hhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.4c  PDB: A:83-207 (gaps) UniProt: 38-207 [INCOMPLETE]                                                                 Exon 1.5  PDB: A:208-306 UniProt: 208-306                                                          Exon 1.6  PDB: A:307-334     Transcript 1
                 1v83 A  83 LPTIHVVTPTYSRPVQKAELTRMANTLLHVPNLHWLVVEDAPRRTPLTARLLRDTGLNYTHLHVETPRNYKL-------RIPRGTMQRNLALRWLRETFPRNSSQPGVVYFADDDNTYSLELFEEMRSTRRVSVWPVAFVGGLRYEAPRVNGAGKVVRWKTVFDPHRPFAIDMAGFAVNLRLILQRSQAYFKLRGVKGGYQESSLLRELVTLNDLEPKAANCTKILVWHTRTEKPVLVNEGKKGFTDPSVEI 334
                                    92       102       112       122       132       142       152 |     162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332  
                                                                                                 154     162                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with B3GA1_HUMAN | Q9P2W7 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:253
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
          B3GA1_HUMAN    82 TLPTIHVVTPTYSRPVQKAELTRMANTLLHVPNLHWLVVEDAPRRTPLTARLLRDTGLNYTHLHVETPRNYKLRGDARDPRIPRGTMQRNLALRWLRETFPRNSSQPGVVYFADDDNTYSLELFEEMRSTRRVSVWPVAFVGGLRYEAPRVNGAGKVVGWKTVFDPHRPFAIDMAGFAVNLRLILQRSQAYFKLRGVKGGYQESSLLRELVTLNDLEPKAANCTKILVWHTRTEKPVLVNEGKKGFTDPSVEI 334
               SCOP domains d1v83b_ B: Beta-1,3-glucuronyltransferase 1, GlcAT-P                                                                                                                                                                                                          SCOP domains
               CATH domains 1v83B00 B:82-334 Spore Coat Polysaccharide Biosynthesis Protein SpsA            ; Chain A                                                                                                                                                                     CATH domains
           Pfam domains (1) -----------------------Glyco_transf_43-1v83B01 B:105-316                                                                                                                                                                                   ------------------ Pfam domains (1)
           Pfam domains (2) -----------------------Glyco_transf_43-1v83B02 B:105-316                                                                                                                                                                                   ------------------ Pfam domains (2)
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh.eeeeee....------------....hhhhhhhhhhhhhhhh.......eeeee.....eehhhhhhhhhh...eee..ee......eeeeee.....eeeee...........hhh.eeeehhhhhhh.............hhhhhhhhhhhhhh.eeehhhhhh...ee........hhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4c  PDB: B:82-207 (gaps) UniProt: 38-207 [INCOMPLETE]                                                                  Exon 1.5  PDB: B:208-306 UniProt: 208-306                                                          Exon 1.6  PDB: B:307-334     Transcript 1
                 1v83 B  82 ALPTIHVVTPTYSRPVQKAELTRMANTLLHVPNLHWLVVEDAPRRTPLTARLLRDTGLNYTHLHVETP------------RIPRGTMQRNLALRWLRETFPRNSSQPGVVYFADDDNTYSLELFEEMRSTRRVSVWPVAFVGGLRYEAPRVNGAGKVVRWKTVFDPHRPFAIDMAGFAVNLRLILQRSQAYFKLRGVKGGYQESSLLRELVTLNDLEPKAANCTKILVWHTRTEKPVLVNEGKKGFTDPSVEI 334
                                    91       101       111       121       131       141       | -         -|      171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
                                                                                             149          162
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B3GA1_HUMAN | Q9P2W7)
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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  1v83
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 Related Entries

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

UniProtKB/Swiss-Prot
        B3GA1_HUMAN | Q9P2W7: 1v82 1v84

(-) Related Entries Specified in the PDB File

1v82 HUMAN GLCAT-P APO FORM
1v84 HUMAN GLCAT-P IN COMPLEX WITH N-ACETYLLACTOSAMINE, UDP, AND MN2+