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(-) Description

Title :  THE STRUCTURE OF HYDROXYPROPYLPHOSPHONIC ACID EPOXIDASE FROM S. WEDMORENIS.
 
Authors :  K. Mcluskey, S. Cameron, W. N. Hunter
Date :  29 Mar 05  (Deposition) - 05 Oct 05  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase, Epoxidase, Cupin, Hth, Cation-Dependant, Zinc, Fosfomycin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Mcluskey, S. Cameron, F. Hammerschmidt, W. N. Hunter
Structure And Reactivity Of Hydroxypropylphosphonic Acid Epoxidase In Fosfomycin Biosynthesis By A Cation- And Flavin-Dependent Mechanism.
Proc. Natl. Acad. Sci. Usa V. 102 14221 2005
PubMed-ID: 16186494  |  Reference-DOI: 10.1073/PNAS.0504314102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPOXIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: STREPTOMYCES WEDMORENSIS
    Organism Taxid: 43759
    Synonym: HYDROXYPROPYLPHOSPHONIC ACID EPOXIDASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1HG4Ligand/IonMERCURY (II) ION
2SO48Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2SO416Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:91 , CYS A:107 , HG A:1200 , HOH A:2125 , VAL B:22 , HOH B:2039BINDING SITE FOR RESIDUE HG A 1199
02AC2SOFTWAREPRO A:91 , ILE A:92 , LEU A:93 , TYR A:105 , CYS A:107 , HG A:1199BINDING SITE FOR RESIDUE HG A 1200
03AC3SOFTWAREHIS A:138 , GLU A:142 , HIS A:180 , HOH A:2192 , HOH A:2195 , HOH A:2197BINDING SITE FOR RESIDUE ZN A 1201
04AC4SOFTWAREARG A:90 , VAL A:121 , PHE A:145 , LYS A:192 , HOH A:2140BINDING SITE FOR RESIDUE SO4 A 1202
05AC5SOFTWAREALA A:114 , PRO A:115 , SER A:116 , HOH A:2138BINDING SITE FOR RESIDUE SO4 A 1203
06AC6SOFTWAREGLN A:55 , ARG A:58 , HOH A:2059 , HOH A:2199 , ASP B:130 , HOH B:2201BINDING SITE FOR RESIDUE SO4 A 1204
07AC7SOFTWAREHIS A:138 , ALA A:139 , HOH A:2201 , HOH A:2202 , GLN B:21 , HOH B:2019BINDING SITE FOR RESIDUE SO4 A 1205
08AC8SOFTWAREVAL A:22 , HOH A:2033 , PRO B:91 , CYS B:107 , HG B:1200BINDING SITE FOR RESIDUE HG B 1199
09AC9SOFTWAREPRO B:91 , ILE B:92 , LEU B:93 , TYR B:105 , CYS B:107 , HG B:1199BINDING SITE FOR RESIDUE HG B 1200
10BC1SOFTWAREHIS B:138 , GLU B:142 , HIS B:180 , HOH B:2248 , HOH B:2249 , HOH B:2250BINDING SITE FOR RESIDUE ZN B 1201
11BC2SOFTWAREHIS A:61 , ASP B:77 , LYS B:112 , HOH B:2133 , HOH B:2251 , HOH B:2252BINDING SITE FOR RESIDUE SO4 B 1202
12BC3SOFTWAREGLN A:21 , HOH A:2019 , HOH A:2032 , HIS B:138 , ALA B:139 , HOH B:2253 , HOH B:2254BINDING SITE FOR RESIDUE SO4 B 1203
13BC4SOFTWAREALA B:114 , PRO B:115 , SER B:116 , HOH B:2167 , HOH B:2255 , HOH B:2256BINDING SITE FOR RESIDUE SO4 B 1204
14BC5SOFTWARETHR A:36 , HOH A:2062 , LYS B:186 , HOH B:2257 , HOH B:2258BINDING SITE FOR RESIDUE SO4 B 1205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BNO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BNO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BNO)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.HPPE_STRWE15-70
 		  2A:15-70
B:15-70
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.HPPE_STRWE15-70
 		  4A:15-70
B:15-70

(-) Exons   (0, 0)

(no "Exon" information available for 2BNO)

(-) 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:191
 aligned with HPPE_STRWE | Q56185 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     
           HPPE_STRWE     4 TKTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
               SCOP domains d2bnoa1 A:4-76                                                           d2bnoa2 A:77-198 H    ydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhh...hhhhh..............hhhhh.ee.----....eeeee..........eeeeeee...hhhhh.........eeeeeee..eeeee......eeeee....eeee.....eeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------HTH_CROC1  PDB: A:15-70 UniProt: 15-70                  -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bno A   4 TKTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILK----NVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
                                    13        23        33        43        53        63        73        83        93|    | 103       113       123       133       143       153       163       173       183       193     
                                                                                                                     94   99                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with HPPE_STRWE | Q56185 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:194
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    
           HPPE_STRWE     5 KTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
               SCOP domains d2bnob1 B:5-76                                                          d2bnob2 B:77-198 Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhh...hhhhh..............hhhhh.eeeeee..eeeeeeee..........eeeeeee...hhhhh........eeeeeeee..eeeee......eeeee....eeee.....eeeee......eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------HTH_CROC1  PDB: B:15-70 UniProt: 15-70                  -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bno B   5 KTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
   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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BNO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BNO)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HPPE_STRWE | Q56185)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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:0016717    oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced to two molecules of water.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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:1901766    phosphinothricin biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphinothricin.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HPPE_STRWE | Q56185: 1zz6 1zz7 1zz8 1zz9 1zzb 1zzc 2bnm 2bnn 3scf 3scg 3sch 4j1w 4j1x

(-) Related Entries Specified in the PDB File

1zz6 CRYSTAL STRUCTURE OF APO-HPPE
1zz7 CRYSTAL STRUCTURE OF FEII HPPE IN COMPLEX WITH SUBSTRATEFORM 1
1zz8 CRYSTAL STRUCTURE OF FEII HPPE IN COMPLEX WITH SUBSTRATEFORM 2
1zz9 CRYSTAL STRUCTURE OF FEII HPPE
1zzb CRYSTAL STRUCTURE OF COII HPPE IN COMPLEX WITH SUBSTRATE
1zzc CRYSTAL STRUCTURE OF COII HPPE IN COMPLEX WITH TRIS BUFFER
2bnm THE STRUCTURE OF HYDROXYPROPYLPHOSPHONIC ACID EPOXIDASE FROM S. WEDMORENIS.
2bnn THE STRUCTURE OF HYDROXYPROPYLPHOSPHONIC ACID EPOXIDASE FROM S. WEDMORENIS IN COMPLEX WITH FOSFOMYCIN