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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN 3-O-SULFOTRANSFERASE-3 WITH BOUND PAP AND TETRASACCHARIDE SUBSTRATE
 
Authors :  A. F. Moon, S. C. Edavettal, J. M. Krahn, E. M. Munoz, M. Negishi, R. J. Lin J. Liu, L. C. Pedersen
Date :  13 May 04  (Deposition) - 31 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Alpha-Beta Motif, Substrate-Binding Cleft, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Moon, S. C. Edavettal, J. M. Krahn, E. M. Munoz, M. Negishi, R. J. Linhardt, J. Liu, L. C. Pedersen
Structural Analysis Of The Sulfotransferase (3-O-Sulfotransferase Isoform 3) Involved In The Biosynthesis Of An Entry Receptor For Herpes Simplex Virus
J. Biol. Chem. V. 279 45185 2004
PubMed-ID: 15304505  |  Reference-DOI: 10.1074/JBC.M405013200

(-) Compounds

Molecule 1 - HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3A1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T3
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: H3-OST-3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE, 3-OST-3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric Unit (6, 9)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2IDS1Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3NA2Ligand/IonSODIUM ION
4SGN2Ligand/IonN,O6-DISULFO-GLUCOSAMINE
5SO41Ligand/IonSULFATE ION
6UAP1Ligand/Ion1,4-DIDEOXY-5-DEHYDRO-O2-SULFO-GLUCURONIC ACID
Biological Unit 1 (5, 7)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2IDS1Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3NA-1Ligand/IonSODIUM ION
4SGN2Ligand/IonN,O6-DISULFO-GLUCOSAMINE
5SO41Ligand/IonSULFATE ION
6UAP1Ligand/Ion1,4-DIDEOXY-5-DEHYDRO-O2-SULFO-GLUCURONIC ACID
Biological Unit 2 (5, 14)
No.NameCountTypeFull Name
1A3P4Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2IDS2Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3NA-1Ligand/IonSODIUM ION
4SGN4Ligand/IonN,O6-DISULFO-GLUCOSAMINE
5SO42Ligand/IonSULFATE ION
6UAP2Ligand/Ion1,4-DIDEOXY-5-DEHYDRO-O2-SULFO-GLUCURONIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:138 , SGN B:2 , IDS B:3 , ARG B:166 , LYS B:215 , GLN B:255 , LYS B:259 , LYS B:366 , THR B:367 , LYS B:368 , ARG B:370 , HOH B:756BINDING SITE FOR RESIDUE UAP B 1
2AC2SOFTWAREUAP B:1 , IDS B:3 , LYS B:161 , GLU B:184 , HIS B:186 , PRO B:217 , SER B:218 , GLN B:255 , LYS B:259 , LYS B:366 , HOH B:721 , HOH B:764 , HOH B:769 , HOH B:786BINDING SITE FOR RESIDUE SGN B 2
3AC3SOFTWAREUAP B:1 , SGN B:2 , SGN B:4 , LYS B:161 , ARG B:190 , ASP B:252 , GLN B:255 , LYS B:259 , NA B:701 , HOH B:781BINDING SITE FOR RESIDUE IDS B 3
4AC4SOFTWAREIDS B:3 , LYS B:161 , ASP B:252 , TYR B:253 , THR B:256 , ARG B:260 , TRP B:283 , SER B:284 , ALA B:285 , NA B:701 , HOH B:748BINDING SITE FOR RESIDUE SGN B 4
5AC5SOFTWARELYS A:161 , HIS A:186 , PRO A:217 , SER A:218 , HOH A:788BINDING SITE FOR RESIDUE SO4 A 700
6AC6SOFTWAREIDS B:3 , SGN B:4 , LYS B:161 , ASP B:252 , THR B:256BINDING SITE FOR RESIDUE NA B 701
7AC7SOFTWARELYS A:161 , ASP A:252 , THR A:256BINDING SITE FOR RESIDUE NA A 702
8AC8SOFTWARELYS A:162 , GLY A:163 , GLY A:164 , THR A:165 , ARG A:166 , ALA A:167 , ARG A:243 , SER A:251 , ILE A:316 , PHE A:349 , PRO A:350 , LEU A:364 , LYS A:368 , GLY A:369 , ARG A:370 , HIS A:372 , HOH A:704 , HOH A:710 , HOH B:707 , HOH B:713 , HOH B:726 , HOH B:739 , HOH B:776BINDING SITE FOR RESIDUE A3P B 602
9AC9SOFTWARELYS B:162 , GLY B:163 , GLY B:164 , THR B:165 , ARG B:166 , ALA B:167 , ARG B:243 , SER B:251 , ILE B:316 , PHE B:349 , PRO B:350 , LEU B:364 , LYS B:368 , GLY B:369 , ARG B:370 , HIS B:372 , HOH B:704 , HOH B:708 , HOH B:710 , HOH B:717 , HOH B:725 , HOH B:753 , HOH B:782BINDING SITE FOR RESIDUE A3P B 603

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:351 -A:363
2B:351 -B:363

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:159 -Val A:160
2Gly B:159 -Val B:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T8U)

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002841101ENSE00001220529chr17:13505244-135038481397HS3SA_HUMAN1-2002002A:136-200
B:136-200		65
65
1.2ENST000002841102ENSE00001013372chr17:13400135-133990061130HS3SA_HUMAN200-4062072A:200-406 (gaps)
B:200-406		207
207

(-) 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:268
 aligned with HS3SA_HUMAN | Q9Y663 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:271
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405 
          HS3SA_HUMAN   136 APPGTLALLLDEGSKQLPQAIIIGVKKGGTRALLEFLRVHPDVRAVGAEPHFFDRSYDKGLAWYRDLMPRTLDGQITMEKTPSYFVTREAPARISAMSKDTKLIVVVRDPVTRAISDYTQTLSKRPDIPTFESLTFKNRTAGLIDTSWSAIQIGIYAKHLEHWLRHFPIRQMLFVSGERLISDPAGELGRVQDFLGLKRIITDKHFYFNKTKGFPCLKKAEGSSRPHCLGKTKGRTHPEIDREVVRRLREFYRPFNLKFYQMTGHDFGWDG 406
               SCOP domains d1t8ua_ A: Heparan sulfate glucosamine 3-O-sulfotransferase 3                                                                                                                                                                                                                   SCOP domains
               CATH domains 1t8uA00 A:136-406 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.ee....eeeee....hhhhhhhhhh....eee..........hhhhhhhhhhhhh.ee....eeeee..hhhhh.hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh....hhhhhhh..---......hhhhhh.hhhhhhhhhh...hhh.eeeeehhhhhhhhhhhhhhhhhhh......hhh.eeee....eeee.......................hhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:136-200 UniProt: 1-200 [INCOMPLETE]             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.2  PDB: A:200-406 (gaps) UniProt: 200-406                                                                                                                                                                Transcript 1 (2)
                 1t8u A 136 PNSGTLALLLDEGSKQLPQAIIIGVKKGGTRALLEFLRVHPDVRAVGAEPHFFDRSYDKGLAWYRDLMPRTLDGQITMEKTPSYFVTREAPARISAMSKDTKLIVVVRDPVTRAISDYTQTLSKRPDIPTFESLTFKN---GLIDTSWSAIQIGIYAKHLEHWLRHFPIRQMLFVSGERLISDPAGELGRVQDFLGLKRIITDKHFYFNKTKGFPCLKKAEGSSRPHCLGKTKGRTHPEIDREVVRRLREFYRPFNLKFYQMTGHDFGWDG 406
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       | - |     285       295       305       315       325       335       345       355       365       375       385       395       405 
                                                                                                                                                                   273 277                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with HS3SA_HUMAN | Q9Y663 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:271
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405 
          HS3SA_HUMAN   136 APPGTLALLLDEGSKQLPQAIIIGVKKGGTRALLEFLRVHPDVRAVGAEPHFFDRSYDKGLAWYRDLMPRTLDGQITMEKTPSYFVTREAPARISAMSKDTKLIVVVRDPVTRAISDYTQTLSKRPDIPTFESLTFKNRTAGLIDTSWSAIQIGIYAKHLEHWLRHFPIRQMLFVSGERLISDPAGELGRVQDFLGLKRIITDKHFYFNKTKGFPCLKKAEGSSRPHCLGKTKGRTHPEIDREVVRRLREFYRPFNLKFYQMTGHDFGWDG 406
               SCOP domains d1t8ub_ B: Heparan sulfate glucosamine 3-O-sulfotransferase 3                                                                                                                                                                                                                   SCOP domains
               CATH domains 1t8uB00 B:136-406 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                          CATH domains
           Pfam domains (1) ----------------Sulfotransfer_1-1t8uB01 B:152-400                                                                                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) ----------------Sulfotransfer_1-1t8uB02 B:152-400                                                                                                                                                                                                                        ------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh......eeeee....hhhhhhhhhh....eee..........hhhhhhhhhhhhh.......eeeee.hhhhhh.hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh....hhhhhheee....ee...hhhhhh.hhhhhhhhhh...hhh.eeeeehhhhhhhhhhhhhhhhhhh......hhh.eeee....eeee.......................hhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:136-200 UniProt: 1-200 [INCOMPLETE]             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.2  PDB: B:200-406 UniProt: 200-406                                                                                                                                                                       Transcript 1 (2)
                 1t8u B 136 PNSGTLALLLDEGSKQLPQAIIIGVKKGGTRALLEFLRVHPDVRAVGAEPHFFDRSYDKGLAWYRDLMPRTLDGQITMEKTPSYFVTREAPARISAMSKDTKLIVVVRDPVTRAISDYTQTLSKRPDIPTFESLTFKNRTAGLIDTSWSAIQIGIYAKHLEHWLRHFPIRQMLFVSGERLISDPAGELGRVQDFLGLKRIITDKHFYFNKTKGFPCLKKAEGSSRPHCLGKTKGRTHPEIDREVVRRLREFYRPFNLKFYQMTGHDFGWDG 406
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HS3SA_HUMAN | Q9Y663)
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:0033872    [heparan sulfate]-glucosamine 3-sulfotransferase 3 activity    Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate.
    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: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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  1t8u
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  HS3SA_HUMAN | Q9Y663
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 Related Entries

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

UniProtKB/Swiss-Prot
        HS3SA_HUMAN | Q9Y663: 1t8t

(-) Related Entries Specified in the PDB File

1bfb CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR WITH BOUND TETRASACCHARIDE
1hy3 CRYSTAL STRUCTURE OF HUMAN ESTROGEN SULFOTRANSFERASE WITH BOUND PAPS SUBSTRATE
1s6t CRYSTAL STRUCTURE OF MURINE 3-O-SULFOTRANSFERASE-1
1t8t CRYSTAL STRUCTURE OF HUMAN 3-O-SULFOTRANSFERASE-3 WITH BOUND PAP