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(-) Description

Title :  CRYSTAL STRUCTURE OF HYP-1 PROTEIN FROM HYPERICUM PERFORATUM (ST JOHN'S WORT) INVOLVED IN HYPERICIN BIOSYNTHESIS
 
Authors :  K. Michalska, H. Fernandes, M. M. Sikorski, M. Jaskolski
Date :  22 Jul 09  (Deposition) - 10 Nov 09  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hypericin, St John'S Wort, Depression, Allergy, Pr-10 Protein, Cytokinin, Plant Hormones, Polyethylene Glycol, Peg, Pathogenesis-Related Protein, Plant Defense, Plant Protein, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Michalska, H. Fernandes, M. M. Sikorski, M. Jaskolski
Crystal Structure Of Hyp-1, A St. John'S Wort Protein Implicated In The Biosynthesis Of Hypericin
J. Struct. Biol. V. 169 161 2010
PubMed-ID: 19853038  |  Reference-DOI: 10.1016/J.JSB.2009.10.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHENOLIC OXIDATIVE COUPLING PROTEIN HYP-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151/D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HYP-1
    Organism Common: ST. JOHN'S WORT
    Organism Scientific: HYPERICUM PERFORATUM
    Organism Taxid: 65561

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 11)

Asymmetric Unit (6, 11)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2CL1Ligand/IonCHLORIDE ION
3PE81Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG45Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2CL-1Ligand/IonCHLORIDE ION
3PE81Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG43Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2CL-1Ligand/IonCHLORIDE ION
3PE8-1Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:56 , VAL B:157 , PHE B:158 , HOH B:198BINDING SITE FOR RESIDUE CL A 400
02AC2SOFTWARELYS A:8 , GLU A:10 , TYR A:141 , HOH A:252 , VAL B:7BINDING SITE FOR RESIDUE PGE A 501
03AC3SOFTWAREARG A:27 , PHE A:39 , TYR A:120BINDING SITE FOR RESIDUE PG4 A 502
04AC4SOFTWAREGLN A:29 , LYS A:33 , ASP A:48 , TYR A:150 , HOH A:230BINDING SITE FOR RESIDUE PE8 A 507
05AC5SOFTWAREGLU A:46 , LYS A:71 , PHE A:87 , HOH A:242 , HOH A:249BINDING SITE FOR RESIDUE PG4 A 508
06AC6SOFTWARELYS A:83 , GLU A:97 , LYS A:98 , HIS A:121 , HOH A:225BINDING SITE FOR RESIDUE PG4 A 509
07AC7SOFTWARELEU B:23 , ARG B:27 , TYR B:84 , TYR B:101 , TYR B:144 , PEG B:505BINDING SITE FOR RESIDUE 1PE B 503
08AC8SOFTWARELEU B:65 , MET B:68 , LEU B:86 , TYR B:120 , LYS B:139 , PEG B:505BINDING SITE FOR RESIDUE PG4 B 504
09AC9SOFTWAREGLN B:35 , LYS B:139 , 1PE B:503 , PG4 B:504BINDING SITE FOR RESIDUE PEG B 505
10BC1SOFTWAREGLN B:29 , LYS B:33 , ALA B:34 , TYR B:150BINDING SITE FOR RESIDUE 1PE B 506
11BC2SOFTWAREPHE B:87 , GLU B:97 , LYS B:98 , HIS B:121 , HOH B:178BINDING SITE FOR RESIDUE PG4 B 510

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:126 -B:126

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IE5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IE5)

(-) Exons   (0, 0)

(no "Exon" information available for 3IE5)

(-) 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:160
 aligned with Q8H1L1_HYPPE | Q8H1L1 from UniProtKB/TrEMBL  Length:159

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
         Q8H1L1_HYPPE     - -MAAYTIVKEEESPTAPHRLFKALVLERHQVLVKAQPHVFKSGEIIEGDGGVGTVTKITFVDGHPLTYMLHKFDEIDAANFYCKYTIFEGDVLRDNIEKVVYEVKLEAVGGGSKGKITVSYHPKPGCTVNEEEVKIGEKKAYEFYKQVEEYLAANPEVFA 159
               SCOP domains d3ie5a_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains 3ie5A00 A:-1-159  [code=3.30.530.20, no name defined]                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..hhhhhhhhhh.hhhhhhhhhh...eeeeeeee.......eeeeee.......eeeeeeeeeehhh.eeeeeeeee.hhh..eeeeeeeeeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ie5 A  -1 TMAAYTIVKEEESPIAPHRLFKALVLERHQVLVKAQPHVFKSGEIIEGDGGVGTVTKITFVDGHPLTYMLHKFDEIDAANFYCKYTLFEGDVLRDNIEKVVYEVKLEAVGGGSKGKITVTYHPKPGCTVNEEEVKIGEKKAYEFYKQVEEYLAANPEVFA 159
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
                            ||                                                                                                                                                              
                           -1|                                                                                                                                                              
                             1                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with Q8H1L1_HYPPE | Q8H1L1 from UniProtKB/TrEMBL  Length:159

    Alignment length:164
                                 1                                                                                                                                                              
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155    
         Q8H1L1_HYPPE     - -----MAAYTIVKEEESPTAPHRLFKALVLERHQVLVKAQPHVFKSGEIIEGDGGVGTVTKITFVDGHPLTYMLHKFDEIDAANFYCKYTIFEGDVLRDNIEKVVYEVKLEAVGGGSKGKITVSYHPKPGCTVNEEEVKIGEKKAYEFYKQVEEYLAANPEVFA 159
               SCOP domains d3ie5b_ B: automated matches                                                                                                                                         SCOP domains
               CATH domains 3ie5B00 B:-5-159  [code=3.30.530.20, no name defined]                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh...eeeeeeee.......eeeeee.......eeeeeeeeeehhh.eeeeeeeee.hhh..eeeeeeeeeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ie5 B  -5 IDPFTMAAYTIVKEEESPIAPHRLFKALVLERHQVLVKAQPHVFKSGEIIEGDGGVGTVTKITFVDGHPLTYMLHKFDEIDAANFYCKYTLFEGDVLRDNIEKVVYEVKLEAVGGGSKGKITVTYHPKPGCTVNEEEVKIGEKKAYEFYKQVEEYLAANPEVFA 159
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155    
                               -1|                                                                                                                                                              
                                 1
   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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IE5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8H1L1_HYPPE | Q8H1L1)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0009607    response to biotic stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8H1L1_HYPPE | Q8H1L1: 4n3e

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