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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TYROSYLPROTEIN SULFOTRANSFERASE-2 COMPLEXED WITH PAP,C4 PEPTIDE, AND PHOSPHATE ION
 
Authors :  T. Teramoto, Y. Fujikawa, Y. Kawaguchi, K. Kurogi, M. Soejima, R. Adach Y. Nakanishi, E. Mishiro-Sato, M. -C. Liu, Y. Sakakibara, M. Suiko, M. Y. Kakuta
Date :  09 Oct 10  (Deposition) - 26 Oct 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,S,T
Keywords :  Sulfotransferase Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Teramoto, Y. Fujikawa, Y. Kawaguchi, K. Kurogi, M. Soejima, R. Adachi, Y. Nakanishi, E. Mishiro-Sato, M. -C. Liu, Y. Sakakibara, M. Suiko, M. Kimura, Y. Kakuta
Crystal Structure Of Human Tyrosylprotein Sulfotransferase-2: Insights Into Substrate-Binding And Catalysis Of Post-Translational Protein Tyrosine Sulfation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN-TYROSINE SULFOTRANSFERASE 2
    Chains: A, B
    EC Number: 2.8.2.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 43-359
    Gene: TPST2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TYROSYLPROTEIN SULFOTRANSFERASE 2, TPST-2
 
Molecule 2 - C4 PEPTIDE
    Chains: S, T
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:78 , SER A:79 , GLY A:80 , THR A:81 , THR A:82 , LEU A:83 , ARG A:183 , SER A:191 , ARG A:195 , TYR A:238 , SER A:285 , GLN A:288 , VAL A:289 , LYS A:291 , PRO A:292 , VAL A:293 , ASN A:294 , ALA A:297 , LYS A:300 , HOH A:367BINDING SITE FOR RESIDUE A3P A 1
2AC2SOFTWAREHOH B:5 , ARG B:78 , SER B:79 , GLY B:80 , THR B:81 , THR B:82 , LEU B:83 , ARG B:183 , SER B:191 , ARG B:195 , TYR B:238 , SER B:285 , GLN B:288 , VAL B:289 , LYS B:291 , PRO B:292 , VAL B:293 , ASN B:294 , ALA B:297 , LYS B:300 , HOH B:363BINDING SITE FOR RESIDUE A3P B 1
3AC3SOFTWAREGLN A:346 , LEU A:349 , LEU B:295 , GLU B:296 , LEU B:298 , SER B:299 , LYS B:300BINDING SITE FOR RESIDUE GOL B 360
4AC4SOFTWAREARG A:118 , LYS B:196 , ARG B:284 , ASP T:1005BINDING SITE FOR RESIDUE PO4 T 1

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:96 -A:156
2A:225 -A:233
3B:96 -B:156
4B:225 -B:233

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:330 -Pro A:331
2Asn B:330 -Pro B:331

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AP2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AP2)

(-) Exons   (0, 0)

(no "Exon" information available for 3AP2)

(-) 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:300
 aligned with TPST2_HUMAN | O60704 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:303
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   
         TPST2_HUMAN     51 ELVMVGTNHVEYRYGKAMPLIFVGGVPRSGTTLMRAMLDAHPEVRCGEETRIIPRVLAMRQAWSKSGREKLRLDEAGVTDEVLDAAMQAFILEVIAKHGEPARVLCNKDPFTLKSSVYLSRLFPNSKFLLMVRDGRASVHSMITRKVTIAGFDLSSYRDCLTKWNKAIEVMYAQCMEVGKEKCLPVYYEQLVLHPRRSLKLILDFLGIAWSDAVLHHEDLIGKPGGVSLSKIERSTDQVIKPVNLEALSKWTGHIPGDVVRDMAQIAPMLAQLGYDPYANPPNYGNPDPFVINNTQRVLKGDY  353
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..---..eee.....eeeeee....hhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..............hhhhhh...............hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ap2 A   51 ELVMVG---VEYRYGKAMPLIFVGGVPRSGTTLMRAMLDAHPEVRCGEETRIIPRVLAMRQAWSKSGREKLRLDEAGVTDEVLDAAMQAFILEVIAKHGEPARVLCNKDPFTLKSSVYLSRLFPNSKFLLMVRDGRASVHSMITRKVTIAGFDLSSYRDCLTKWNKAIEVMYAQCMEVGKEKCLPVYYEQLVLHPRRSLKLILDFLGIAWSDAVLHHEDLIGKPGGVSLSKIERSTDQVIKPVNLEALSKWTGHIPGDVVRDMAQIAPMLAQLGYDPYANPPNYGNPDPFVINNTQRVLKGDY  353
                                 |  60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   
                                56  60                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with TPST2_HUMAN | O60704 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:301
                                    61        71        81        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       341       351 
         TPST2_HUMAN     52 LVMVGTNHVEYRYGKAMPLIFVGGVPRSGTTLMRAMLDAHPEVRCGEETRIIPRVLAMRQAWSKSGREKLRLDEAGVTDEVLDAAMQAFILEVIAKHGEPARVLCNKDPFTLKSSVYLSRLFPNSKFLLMVRDGRASVHSMITRKVTIAGFDLSSYRDCLTKWNKAIEVMYAQCMEVGKEKCLPVYYEQLVLHPRRSLKLILDFLGIAWSDAVLHHEDLIGKPGGVSLSKIERSTDQVIKPVNLEALSKWTGHIPGDVVRDMAQIAPMLAQLGYDPYANPPNYGNPDPFVINNTQRVLKGD  352
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----..........eeeee.....hhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..............hhhhhh...............hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ap2 B   52 LVMV----VEYRYGKAMPLIFVGGVPRSGTTLMRAMLDAHPEVRCGEETRIIPRVLAMRQAWSKSGREKLRLDEAGVTDEVLDAAMQAFILEVIAKHGEPARVLCNKDPFTLKSSVYLSRLFPNSKFLLMVRDGRASVHSMITRKVTIAGFDLSSYRDCLTKWNKAIEVMYAQCMEVGKEKCLPVYYEQLVLHPRRSLKLILDFLGIAWSDAVLHHEDLIGKPGGVSLSKIERSTDQVIKPVNLEALSKWTGHIPGDVVRDMAQIAPMLAQLGYDPYANPPNYGNPDPFVINNTQRVLKGD  352
                               |    61        71        81        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       341       351 
                              55   60                                                                                                                                                                                                                                                                                                    


Chain S from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                3ap2 S 1001 EDFEDYEFD 1009


Chain T from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                3ap2 T 1001 EDFEDYEFD 1009
   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  (0, 0)

(no "SCOP Domain" information available for 3AP2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AP2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AP2)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPST2_HUMAN | O60704)
molecular function
    GO:0008476    protein-tyrosine sulfotransferase activity    Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + protein tyrosine = adenosine 3',5'-bisphosphate + protein tyrosine-O-sulfate.
    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:0006478    peptidyl-tyrosine sulfation    The sulfation of peptidyl-tyrosine residues to form peptidyl-O4'-sulfo-L-tyrosine.
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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        TPST2_HUMAN | O60704: 3ap1 3ap3

(-) Related Entries Specified in the PDB File

3ap1 3ap3