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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CHOLESTEROL SULFOTRANSFERASE (SULT2B1B) IN THE PRESENCE OF DHEA AND PAP
 
Authors :  K. A. Lee, H. Fuda, Y. C. Lee, M. Negishi, C. A. Strott, L. C. Pedersen
Date :  23 Jul 03  (Deposition) - 11 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Sulfotransferase, Dhea, Pap, Sult2B1B (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. A. Lee, H. Fuda, Y. C. Lee, M. Negishi, C. A. Strott, L. C. Pedersen
Crystal Structure Of Human Cholesterol Sulfotransferase (Sult2B1B) In The Presence Of Pregnenolone And 3'-Phosphoadenosine 5'-Phosphate. Rationale For Specificity Differences Between Prototypical Sult2A1 And The Sult2Bg1 Isoforms.
J. Biol. Chem. V. 278 44593 2003
PubMed-ID: 12923182  |  Reference-DOI: 10.1074/JBC.M308312200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SULFOTRANSFERASE FAMILY, CYTOSOLIC, 2B, MEMBER 1 ISOFORM B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T3
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSULT2B1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSULT2B1B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1A3P1Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2AND1Ligand/Ion3-BETA-HYDROXY-5-ANDROSTEN-17-ONE
3NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:160 , ALA A:163 , LEU A:166 , HOH A:449 , HOH A:450BINDING SITE FOR RESIDUE NA A 313
2AC2SOFTWARELYS A:70 , SER A:71 , GLY A:72 , THR A:73 , THR A:74 , TRP A:75 , ARG A:147 , SER A:155 , TYR A:210 , SER A:244 , PHE A:246 , MET A:249 , PHE A:272 , LEU A:273 , ARG A:274 , LYS A:275 , GLY A:276 , HOH A:402 , HOH A:407 , HOH A:410 , HOH A:416 , HOH A:448BINDING SITE FOR RESIDUE A3P A 314
3AC3SOFTWARETYR A:44 , TRP A:98 , TRP A:103 , THR A:106 , HIS A:125 , GLN A:165 , TYR A:257 , LEU A:260 , HOH A:416BINDING SITE FOR RESIDUE AND A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q22)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q22)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020887L51SST2B1_HUMANPolymorphism16982149AL51S
2UniProtVAR_021988V240IST2B1_HUMANPolymorphism2302947AV240I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q22)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002015861ENSE00001244662chr19:49055429-49055580152ST2B1_HUMAN1-24241A:18-247
1.2bENST000002015862bENSE00001244643chr19:49079198-49079340143ST2B1_HUMAN24-72491A:24-7249
1.3ENST000002015863ENSE00000717419chr19:49090486-49090694209ST2B1_HUMAN72-141701A:72-141 (gaps)70
1.4ENST000002015864ENSE00000717418chr19:49094866-49094992127ST2B1_HUMAN142-184431A:142-18443
1.5ENST000002015865ENSE00000717417chr19:49095979-4909607395ST2B1_HUMAN184-215321A:184-21532
1.6ENST000002015866ENSE00001244683chr19:49099996-49100176181ST2B1_HUMAN216-276611A:216-27661
1.7ENST000002015867ENSE00000896514chr19:49102392-49102683292ST2B1_HUMAN276-365901A:276-31136

(-) 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:291
 aligned with ST2B1_HUMAN | O00204 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:294
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    
          ST2B1_HUMAN    18 DDISEISQKLPGEYFRYKGVPFPVGLYSLESISLAENTQDVRDDDIFIITYPKSGTTWMIEIICLILKEGDPSWIRSVPIWERAPWCETIVGAFSLPDQYSPRLMSSHLPIQIFTKAFFSSKAKVIYMGRNPRDVVVSLYHYSKIAGQLKDPGTPDQFLRDFLKGEVQFGSWFDHIKGWLRMKGKDNFLFITYEELQQDLQGSVERICGFLGRPLGKEALGSVVAHSTFSAMKANTMSNYTLLPPSLLDHRRGAFLRKGVCGDWKNHFTVAQSEAFDRAYRKQMRGMPTFPWDE 311
               SCOP domains d1q22a_ A: Cholesterol sulfotransferase sult2b1b                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1q22A00 A:18-311 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------Sulfotransfer_1-1q22A01 A:60-305                                                                                                                                                                                                                      ------ Pfam domains
         Sec.struct. author hhhhhhhhh....eeee..eeee....hhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhh..---..eeee.......hhhhh....eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..........................hhhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------S--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.1    -----------------------------------------------Exon 1.3  PDB: A:72-141 (gaps) UniProt: 72-141                        Exon 1.4  PDB: A:142-184 UniProt: 142-184  -------------------------------Exon 1.6  PDB: A:216-276 UniProt: 216-276                    ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.2b  PDB: A:24-72 UniProt: 24-72           ---------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:184-215        ------------------------------------------------------------Exon 1.7  PDB: A:276-311             Transcript 1 (2)
                 1q22 A  18 SDISEISQKLPGEYFRYKGVPFPVGLYSLESISLAENTQDVRDDDIFIITYPKSGTTWMIEIICLILKEGDPSWIRSVPIWERAPWCETIVGAFSLPD---PRLMSSHLPIQIFTKAFFSSKAKVIYMGRNPRDVVVSLYHYSKIAGQLKDPGTPDQFLRDFLKGEVQFGSWFDHIKGWLRMKGKDNFLFITYEELQQDLQGSVERICGFLGRPLGKEALGSVVAHSTFSAMKANTMSNYTLLPPSLLDHRRGAFLRKGVCGDWKNHFTVAQSEAFDRAYRKQMRGMPTFPWDE 311
                                    27        37        47        57        67        77        87        97       107       | - |     127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    
                                                                                                                           115 119                                                                                                                                                                                                

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ST2B1_HUMAN | O00204)
molecular function
    GO:0004027    alcohol sulfotransferase activity    Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + an alcohol = adenosine 3',5'-bisphosphate + an alkyl sulfate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0050294    steroid sulfotransferase activity    Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + a phenolic steroid = adenosine 3',5'-bisphosphate + steroid O-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:0050427    3'-phosphoadenosine 5'-phosphosulfate metabolic process    The chemical reactions and pathways involving 3'-phosphoadenosine 5'-phosphosulfate, a naturally occurring mixed anhydride. It is an intermediate in the formation of a variety of sulfo compounds in biological systems.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ST2B1_HUMAN | O002041q1q 1q1z 1q20

(-) Related Entries Specified in the PDB File

1q1q SULT2B1A AND SULT2B1B DIFFER ONLY AT N TERMINUS BY 8 AMINO ACIDS IN 2B1A AND 23 AMINO ACIDS IN 2B1B
1q1z SULT2B1B WITH PAP BOUND
1q20 SULT2B1B WITH PAP AND PREGNENOLONE BOUND