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(-) Description

Title :  STRUCTURE OF FE2-HPPD BOUND TO NTBC
 
Authors :  J. Brownlee, K. Johnson-Winters, D. H. T. Harrison, G. R. Moran
Date :  28 Apr 04  (Deposition) - 15 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Triketone Inhibitor, Dioxygenase, Iron, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Brownlee, K. Johnson-Winters, D. H. T. Harrison, G. R. Moran
Structure Of The Ferrous Form Of (4-Hydroxyphenyl)Pyruvate Dioxygenase From Streptomyces Avermitilis In Complex With The Therapeutic Herbicide, Ntbc
Biochemistry V. 43 6370 2004
PubMed-ID: 15157070  |  Reference-DOI: 10.1021/BI049317S
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4-HYDROXYPHENYLPYRUVATE DIOXYGENASE
    Chains: A, B
    EC Number: 1.13.11.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Gene: HPD, SAV5149
    Organism Scientific: STREPTOMYCES AVERMITILIS
    Organism Taxid: 33903
    Synonym: 4HPPD, HPD, HPPDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FE22Ligand/IonFE (II) ION
2NTD2Ligand/Ion2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:187 , HIS B:270 , GLU B:349 , NTD B:550 , HOH B:874BINDING SITE FOR RESIDUE FE2 B 430
2AC2SOFTWAREHIS A:187 , HIS A:270 , GLU A:349 , NTD A:551BINDING SITE FOR RESIDUE FE2 A 431
3AC3SOFTWAREHIS A:187 , SER A:230 , PRO A:243 , ASN A:245 , HIS A:270 , LEU A:323 , PHE A:336 , PHE A:347 , GLU A:349 , PHE A:359 , GLY A:360 , ASN A:363 , PHE A:364 , LEU A:367 , FE2 A:431BINDING SITE FOR RESIDUE NTD A 551
4AC4SOFTWAREHIS B:187 , SER B:230 , PRO B:243 , ASN B:245 , HIS B:270 , LEU B:323 , PHE B:336 , PHE B:347 , GLU B:349 , PHE B:359 , GLY B:360 , ASN B:363 , PHE B:364 , LEU B:367 , FE2 B:430BINDING SITE FOR RESIDUE NTD B 550

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T47)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T47)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T47)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VOCPS51819 Vicinal oxygen chelate (VOC) domain profile.HPPD_STRAW22-156
 
184-338
 		  4A:22-156
B:22-156
A:184-338
B:184-338

(-) Exons   (0, 0)

(no "Exon" information available for 1T47)

(-) 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:362
 aligned with HPPD_STRAW | Q53586 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:362
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375  
           HPPD_STRAW    16 DPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSARFVLTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYELKDEHGTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVAAAPIVEPPAHRTFQAIDHCVGNVELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAKKKSQIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDTPDSYYDTLGEWVGDTRVPVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEAIEREQEK 377
               SCOP domains d1t47a1 A:16-178 4-hydroxyphenylpyruvate dioxygenase, HppD                                                                                                         d1t47a2 A:179-377 4-hydroxyphenylpyruvate dioxygenase, HppD                                                                                                                                             SCOP domains
               CATH domains 1t47A01 A:16-178 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                   1t47A02 A:179-377 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..hhhhhhhhhhhh...eeeeeehhhhh...eeeeeeee..eeeeeeee....hhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhh...eeeeeeeeee..eeeeeeeee.....eeeeeeeeee........ee..............eeeeeeee....hhhhhhhhhhhhhh.ee.....hhhhhh....eeeeeee......eeeeeee......hhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.......hhhhh.hhhhhhh....hhhhhhhhh.eeee....eeeeee..........eeeeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------VOC  PDB: A:22-156 UniProt: 22-156                                                                                                     ---------------------------VOC  PDB: A:184-338 UniProt: 184-338                                                                                                                       --------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t47 A  16 DPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSARFVLTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYELKDEHGTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVAAAPIVEPPAHRTFQAIDHCVGNVELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAKKKSQIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDTPDSYYDTLGEWVGDTRVPVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEAIEREQEK 377
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375  


Chain B from PDB  Type:PROTEIN  Length:362
 aligned with HPPD_STRAW | Q53586 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:362
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375  
           HPPD_STRAW    16 DPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSARFVLTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYELKDEHGTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVAAAPIVEPPAHRTFQAIDHCVGNVELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAKKKSQIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDTPDSYYDTLGEWVGDTRVPVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEAIEREQEK 377
               SCOP domains d1t47b1 B:16-178 4-hydroxyphenylpyruvate dioxygenase, HppD                                                                                                         d1t47b2 B:179-377 4-hydroxyphenylpyruvate dioxygenase, HppD                                                                                                                                             SCOP domains
               CATH domains 1t47B01 B:16-178 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                   1t47B02 B:179-377 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                                                       CATH domains
           Pfam domains (1) ------------Glyoxalase_2-1t47B03 B:28-147                                                                                           ------------------------------------Glyoxalase-1t47B01 B:184-335                                                                                                                            ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------Glyoxalase_2-1t47B04 B:28-147                                                                                           ------------------------------------Glyoxalase-1t47B02 B:184-335                                                                                                                            ------------------------------------------ Pfam domains (2)
         Sec.struct. author ......eeeeeeee..hhhhhhhhhhhh...eeeeeehhhhh...eeeeeeee..eeeeeeee....hhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhh...eeeeeeeeee..eeeeeeeee.....eeeeee............ee..............eeeeeeee....hhhhhhhhhhhhh..eeeeeeehhhhhhhh..eeeeeee......eeeeeee......hhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh........hhhhhhhhhhhh....hhhhhhhhh.eeeee..eeeeeee..........eeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------VOC  PDB: B:22-156 UniProt: 22-156                                                                                                     ---------------------------VOC  PDB: B:184-338 UniProt: 184-338                                                                                                                       --------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t47 B  16 DPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSARFVLTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYELKDEHGTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVAAAPIVEPPAHRTFQAIDHCVGNVELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAKKKSQIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDTPDSYYDTLGEWVGDTRVPVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEAIEREQEK 377
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Glyoxalase (58)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HPPD_STRAW | Q53586)
molecular function
    GO:0003868    4-hydroxyphenylpyruvate dioxygenase activity    Catalysis of the reaction: 4-hydroxyphenylpyruvate + O2 = homogentisate + CO2.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016701    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and molecular oxygen is incorporated into a donor.
biological process
    GO:0006559    L-phenylalanine catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
    GO:0009072    aromatic amino acid family metabolic process    The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006572    tyrosine catabolic process    The chemical reactions and pathways resulting in the breakdown of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.

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  1t47
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