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(-) Description

Title :  CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE
 
Authors :  M. Miyano, H. Ago
Date :  14 Dec 98  (Deposition) - 13 Oct 99  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  1,2
Keywords :  Hematopoietic Prostaglandin D Synthase, Pgds, Gst, Sigma-Class Gst, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kanaoka, H. Ago, E. Inagaki, T. Nanayama, M. Miyano, R. Kikuno, Y. Fujii, N. Eguchi, H. Toh, Y. Urade, O. Hayaishi
Cloning And Crystal Structure Of Hematopoietic Prostaglandi D Synthase.
Cell(Cambridge, Mass. ) V. 90 1085 1997
PubMed-ID: 9323136  |  Reference-DOI: 10.1016/S0092-8674(00)80374-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
    Cellular Location: CYTOPLASM
    Chains: 1, 2
    EC Number: 5.3.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Cellular Location: CYTOPLASMIC
    Expression System Gene: DE3
    Expression System Strain: BL21
    Expression System Taxid: 469008
    Expression System Variant: DE3
    Expression System Vector: PT7-7
    Organ: SPLEEN
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: HPGDS, SPLEEN TYPE PGDS, GLUTATHIONE DEPENDENT PGDS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : 12

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR 1:8 , ARG 1:14 , TRP 1:39 , LYS 1:43 , LYS 1:50 , ILE 1:51 , GLN 1:63 , SER 1:64 , HOH 1:320 , ASP 2:97BINDING SITE FOR RESIDUE GSH 1 301
2AC2SOFTWAREASP 1:97 , TYR 2:8 , ARG 2:14 , TRP 2:39 , LYS 2:43 , LYS 2:50 , ILE 2:51 , GLN 2:63 , SER 2:64 , HOH 2:311 , HOH 2:323BINDING SITE FOR RESIDUE GSH 2 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PD2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile 1:51 -Pro 1:52
2Ile 2:51 -Pro 2:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PD2)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_NTERPS50404 Soluble glutathione S-transferase N-terminal domain profile.HPGDS_RAT2-79
 		  21:2-79
2:2-79
2GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.HPGDS_RAT81-199
 		  21:81-199
2:81-199

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000088261ENSRNOE00000060741chr4:94636147-94635796352HPGDS_RAT-00--
1.2ENSRNOT000000088262ENSRNOE00000060859chr4:94629309-94629168142HPGDS_RAT1-454521:1-45
2:1-45		45
45
1.3ENSRNOT000000088263ENSRNOE00000061100chr4:94626200-9462610893HPGDS_RAT45-763221:45-76
2:45-76		32
32
1.4ENSRNOT000000088264ENSRNOE00000061216chr4:94622786-94622677110HPGDS_RAT76-1123721:76-112
2:76-112		37
37
1.5ENSRNOT000000088265ENSRNOE00000061376chr4:94615216-9461511899HPGDS_RAT113-1453321:113-145
2:113-145		33
33
1.6ENSRNOT000000088266ENSRNOE00000061562chr4:94611985-94611611375HPGDS_RAT146-1995421:146-199
2:146-199		54
54

(-) 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 1 from PDB  Type:PROTEIN  Length:199
 aligned with HPGDS_RAT | O35543 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
            HPGDS_RAT     1 MPNYKLLYFNMRGRAEIIRYIFAYLDIKYEDHRIEQADWPKIKPTLPFGKIPVLEVEGLTLHQSLAIARYLTKNTDLAGKTELEQCQVDAVVDTLDDFMSLFPWAEENQDLKERTFNDLLTRQAPHLLKDLDTYLGDKEWFIGNYVTWADFYWDICSTTLLVLKPDLLGIYPRLVSLRNKVQAIPAISAWILKRPQTKL 199
               SCOP domains d1pd212 1:1-75 Class sigma GST                                             d1pd211 1:76-199 Class sigma GST                                                                                             SCOP domains
               CATH domains 1pd2101 1:1-75,1:184-199 Glutaredoxin                                      1pd2102 1:76-183  [code=1.20.1050.10, no name defined]                                                      1pd2101          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhh.......eeee..eeee.hhhhhhhhh...hhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhh............hhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GST_NTER  PDB: 1:2-79 UniProt: 2-79                                           -GST_CTER  PDB: 1:81-199 UniProt: 81-199                                                                                 PROSITE
           Transcript 1 (1) Exon 1.2  PDB: 1:1-45 UniProt: 1-45          ------------------------------Exon 1.4  PDB: 1:76-112              Exon 1.5  PDB: 1:113-145         Exon 1.6  PDB: 1:146-199 UniProt: 146-199              Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3  PDB: 1:45-76          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1pd2 1   1 MPNYKLLYFNMRGRAEIIRYIFAYLDIKYEDHRIEQADWPKIKPTLPFGKIPVLEVEGLTLHQSLAIARYLTKNTDLAGKTELEQCQVDAVVDTLDDFMSLFPWAEENQDLKERTFNDLLTRQAPHLLKDLDTYLGDKEWFIGNYVTWADFYWDICSTTLLVLKPDLLGIYPRLVSLRNKVQAIPAISAWILKRPQTKL 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         


Chain 2 from PDB  Type:PROTEIN  Length:199
 aligned with HPGDS_RAT | O35543 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
            HPGDS_RAT     1 MPNYKLLYFNMRGRAEIIRYIFAYLDIKYEDHRIEQADWPKIKPTLPFGKIPVLEVEGLTLHQSLAIARYLTKNTDLAGKTELEQCQVDAVVDTLDDFMSLFPWAEENQDLKERTFNDLLTRQAPHLLKDLDTYLGDKEWFIGNYVTWADFYWDICSTTLLVLKPDLLGIYPRLVSLRNKVQAIPAISAWILKRPQTKL 199
               SCOP domains d1pd222 2:1-75 Class sigma GST                                             d1pd221 2:76-199 Class sigma GST                                                                                             SCOP domains
               CATH domains 1pd2201 2:1-75,2:184-199 Glutaredoxin                                      1pd2202 2:76-183  [code=1.20.1050.10, no name defined]                                                      1pd2201          CATH domains
           Pfam domains (1) ---GST_N-1pd2203 2:4-73                                                  ------------GST_C-1pd2201 2:86-185                                                                              -------------- Pfam domains (1)
           Pfam domains (2) ---GST_N-1pd2204 2:4-73                                                  ------------GST_C-1pd2202 2:86-185                                                                              -------------- Pfam domains (2)
         Sec.struct. author ...eeeeee......hhhhhhhhh.....eeeee.hhhhhhhhhh.......eeee..eeee.hhhhhhhh....hhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhh............hhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GST_NTER  PDB: 2:2-79 UniProt: 2-79                                           -GST_CTER  PDB: 2:81-199 UniProt: 81-199                                                                                 PROSITE
           Transcript 1 (1) Exon 1.2  PDB: 2:1-45 UniProt: 1-45          ------------------------------Exon 1.4  PDB: 2:76-112              Exon 1.5  PDB: 2:113-145         Exon 1.6  PDB: 2:146-199 UniProt: 146-199              Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3  PDB: 2:45-76          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1pd2 2   1 MPNYKLLYFNMRGRAEIIRYIFAYLDIKYEDHRIEQADWPKIKPTLPFGKIPVLEVEGLTLHQSLAIARYLTKNTDLAGKTELEQCQVDAVVDTLDDFMSLFPWAEENQDLKERTFNDLLTRQAPHLLKDLDTYLGDKEWFIGNYVTWADFYWDICSTTLLVLKPDLLGIYPRLVSLRNKVQAIPAISAWILKRPQTKL 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GST_C (118)
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain 1,2   (HPGDS_RAT | O35543)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0004667    prostaglandin-D synthase activity    Catalysis of the reaction: prostaglandin H(2) = prostaglandin D(2).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    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:2000255    negative regulation of male germ cell proliferation    Any process that stops, prevents or reduces the frequency, rate or extent of male germ cell proliferation.
    GO:0001516    prostaglandin biosynthetic process    The chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring.
    GO:0006693    prostaglandin metabolic process    The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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