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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPARAN SULFATE 3-O-SULFOTRANSFERASE ISOFORM 1 IN THE PRESENCE OF PAP
 
Authors :  S. Thorp, K. A. Lee, M. Negishi, R. J. Linhardt, J. Liu, L. C. Pedersen
Date :  25 May 04  (Deposition) - 01 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Sulfotransferase, Heparan Sulfate, Pap, Papss (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Edavettal, K. A. Lee, M. Negishi, R. J. Linhardt, J. Liu, L. C. Pedersen
Crystal Structure And Mutational Analysis Of Heparan Sulfate 3-O-Sulfotransferase Isoform 1
J. Biol. Chem. V. 279 25789 2004
PubMed-ID: 15060080  |  Reference-DOI: 10.1074/JBC.M401089200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEPARAN SULFATE (GLUCOSAMINE) 3-O- SULFOTRANSFERASE 1
    Chains: A, B, C
    EC Number: 2.8.2.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: G48-H311
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1A3P3Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:72 , GLU A:90 , LYS A:123 , LYS A:274 , HOH A:633 , HOH A:681BINDING SITE FOR RESIDUE SO4 A 601
2AC2SOFTWAREARG B:72 , GLU B:90 , LYS B:123 , LYS B:274 , HOH B:700BINDING SITE FOR RESIDUE SO4 B 602
3AC3SOFTWARELYS A:68 , GLY A:69 , GLY A:70 , THR A:71 , ARG A:72 , ALA A:73 , ARG A:151 , SER A:159 , ILE A:225 , PHE A:258 , TYR A:259 , LEU A:270 , LYS A:274 , GLY A:275 , ARG A:276 , HOH A:608 , HOH A:654 , HOH A:674 , HOH A:676 , HOH A:683BINDING SITE FOR RESIDUE A3P A 602
4AC4SOFTWAREHOH A:636 , HOH A:637 , HOH A:638 , LYS B:68 , GLY B:69 , GLY B:70 , THR B:71 , ARG B:72 , ALA B:73 , ARG B:151 , SER B:159 , ILE B:225 , PHE B:258 , TYR B:259 , LEU B:270 , LYS B:274 , GLY B:275 , ARG B:276 , HIS B:278BINDING SITE FOR RESIDUE A3P A 603
5AC5SOFTWARELYS C:68 , GLY C:69 , GLY C:70 , THR C:71 , ARG C:72 , ALA C:73 , ARG C:151 , SER C:159 , ILE C:225 , PHE C:258 , TYR C:259BINDING SITE FOR RESIDUE A3P A 604

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:260 -A:269
2B:260 -B:269
3C:260 -C:269

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:65 -Val A:66
2Gly B:65 -Val B:66
3Gly C:65 -Val C:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VKJ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VKJ)

(-) 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:258
 aligned with HS3S1_MOUSE | O35310 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:258
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        
          HS3S1_MOUSE    54 STQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMRDGRLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHPQVDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
               SCOP domains d1vkja_ A: Heparan sulfate 3-O-sulfotransferase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1vkjA00 A:54-311 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee....eeeee....hhhhhhhhhhh...eee.........hhhhhh.hhhhhhhh..ee....eeeee.hhhh...hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhee..ee...hhhhhh.hhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhhhhhhh.....hhh.eeee....eeeeee..eee.............hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vkj A  54 STQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMRDGRLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHPQVDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with HS3S1_MOUSE | O35310 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:258
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        
          HS3S1_MOUSE    54 STQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMRDGRLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHPQVDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
               SCOP domains d1vkjb_ B: Heparan sulfate 3-O-sulfotransferase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1vkjB00 B:54-311 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee....eeeee....hhhhhhhhhh....eee.........hhhhhhhhhhhhhhh..ee....eeeee.hhhhhh.hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhee..ee...hhhhhhhhhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhhhhhh......hhh.eeee....eeee....................hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vkj B  54 STQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMRDGRLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHPQVDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        


Chain C from PDB  Type:PROTEIN  Length:247
 aligned with HS3S1_MOUSE | O35310 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:258
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        
          HS3S1_MOUSE    54 STQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMRDGRLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHPQVDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
               SCOP domains d1vkjc_ C: Heparan sulfate 3-O-sulfotransferase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1vkjC00 C:54-311 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                              CATH domains
           Pfam domains (1) ----Sulfotransfer_1-1vkjC01 C:58-302                                                                                                                                                                                                                     --------- Pfam domains (1)
           Pfam domains (2) ----Sulfotransfer_1-1vkjC02 C:58-302                                                                                                                                                                                                                     --------- Pfam domains (2)
           Pfam domains (3) ----Sulfotransfer_1-1vkjC03 C:58-302                                                                                                                                                                                                                     --------- Pfam domains (3)
         Sec.struct. author .ee....eeeee....hhhhhhhhhh....eee.........hhhhhhhhhhhhhhhh.ee....eeeee..hhhhh.hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhee..ee......hhhhhhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhhhhhhh.....hhh.eeee....eeee........-----------.hhhhhhhhh.hhh....hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vkj C  54 STQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMRDGRLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRC-----------VDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263     |   -       283       293       303        
                                                                                                                                                                                                                                                 269         281
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (HS3S1_MOUSE | O35310)
molecular function
    GO:0008467    [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity    Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate. The [heparan sulfate]-glucosamine 3-sulfate has a substrate consensus sequence of Glc(N2S>NAc)+/-6S GlcA GlcN2S*+/-6S GlcA>IdoA+/-2S Glc(N2S/NAc)+/-6S.
    GO:0008146    sulfotransferase activity    Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3'-phosphoadenosine 5'-phosphate.
    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.
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:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.

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  1vkj
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 Related Entries

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

UniProtKB/Swiss-Prot
        HS3S1_MOUSE | O35310: 3uan

(-) Related Entries Specified in the PDB File

1nst CRYSTAL STRUCTURE OF SULFOTRANSFERASE DOMAIN OF N- DEACETYLASE/N-SULFOTRANSFERASE 1