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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HEPARAN SULFATE GLUCOSAMINE 3-O-SULFOTRANSFERASE 1 IN COMPLEX WITH PAP
 
Authors :  A. Dong, L. Dombrovski, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date :  19 May 05  (Deposition) - 07 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Sgc; Sulfotransferase Hs3St1, Structural Genomics, Structural Genomics Consortium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dong, L. Dombrovski, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
Crystal Structure Of Human Heparan Sulfate Glucosamine 3-O-Sulfotransferase 1 In Complex With Pap
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEPARAN SULFATE GLUCOSAMINE 3-O-SULFOTRANSFERASE 1
    Chains: A
    EC Number: 2.8.2.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HS3ST1, 3OST, 3OST1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SULFOTRANSFERASE HS3ST1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1A3P1Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:31 , GLY A:33 , THR A:34 , ARG A:35 , ALA A:36 , ARG A:114 , SER A:122 , ILE A:188 , PHE A:221 , TYR A:222 , LEU A:233 , LYS A:237 , GLY A:238 , ARG A:239 , HIS A:241 , HOH A:313 , HOH A:316 , HOH A:320 , HOH A:368 , HOH A:371BINDING SITE FOR RESIDUE A3P A 301

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:223 -A:232

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:28 -Val A:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052529K295RHS3S1_HUMANPolymorphism34719057AK262R
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000000025961aENSE00001287055chr4:11431389-114303231067HS3S1_HUMAN-00--
1.3bENST000000025963bENSE00002024145chr4:11401737-113947746964HS3S1_HUMAN1-3433431A:12-274263

(-) 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:263
 aligned with HS3S1_HUMAN | O14792 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:263
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
          HS3S1_HUMAN    45 VAPNGSAQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSHGLGWYLSQMPFSWPHQLTVEKTPAYFTSPKVPERVYSMNPSIRLLLILRDPSERVLSDYTQVFYNHMQKHKPYPSIEEFLVRDGRLNVDYKALNRSLYHVHMQNWLRFFPLRHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGRDRCLHESKGRAHPQVDPKLLNKLHEYFHEPNKKFFELVGRTFDWH 307
               SCOP domains d1zrha_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1zrhA00 A:12-274 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                   CATH domains
               Pfam domains ---------Sulfotransfer_1-1zrhA01 A:21-265                                                                                                                                                                                                                     --------- Pfam domains
         Sec.struct. author ......ee....eee......hhhhhhhhhh....eee.........hhhhhhhhhhhhhhh..ee....eeeee.hhhhhh.hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhh.....hhhhhhee..ee...hhhhhhhhhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhhhhhh......hhh.eeee....eeeeee..eee.............hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:12-274 UniProt: 1-343 [INCOMPLETE]                                                                                                                                                                                                                    Transcript 1
                 1zrh A  12 VAPNGSAQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSHGLGWYLSQMPFSWPHQLTVEKTPAYFTSPKVPERVYSMNPSIRLLLILRDPSERVLSDYTQVFYNHMQKHKPYPSIEEFLVRDGRLNVDYKALNRSLYHVHMQNWLRFFPLRHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGRDRCLHESKGRAHPQVDPKLLNKLHEYFHEPNKKFFELVGRTFDWH 274
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HS3S1_HUMAN | O14792)
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.
biological process
    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.
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.
    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.

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