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(-) Description

Title :  CRYSTAL STRUCTURE OF FE(II)-HPPE WITH ALTERNATIVE SUBSTRATE (R)-1-HPP
 
Authors :  C. L. Drennan, M. Dey
Date :  03 Feb 13  (Deposition) - 03 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C  (4x)
Keywords :  Hydroxypropylphosphonic Acid Epoxidase, 1, 2-Phosphono Migration, Mononuclear Non-Heme Iron Enzyme, Metal Binding Protein, Cupin Fold, Phosphono Migration (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Chang, M. Dey, P. Liu, S. O. Mansoorabadi, S. J. Moon, Z. K. Zhao, C. L. Drennan, H. W. Liu
Mechanistic Studies Of An Unprecedented Enzyme-Catalysed 1, 2-Phosphono-Migration Reaction.
Nature V. 496 114 2013
PubMed-ID: 23552950  |  Reference-DOI: 10.1038/NATURE11998

(-) Compounds

Molecule 1 - EPOXIDASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPL001
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: METAL AND SUBSTRATE BINDING DOMAINS (UNP RESIDUES 1-198)
    Gene: FOM4
    Organism Scientific: STREPTOMYCES WEDMORENSIS
    Organism Taxid: 43759

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): AB 
Biological Unit 2 (4x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1FE23Ligand/IonFE (II) ION
2FFQ3Ligand/Ion[(1R)-1-HYDROXYPROPYL]PHOSPHONIC ACID
3GOL4Ligand/IonGLYCEROL
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2FFQ4Ligand/Ion[(1R)-1-HYDROXYPROPYL]PHOSPHONIC ACID
3GOL6Ligand/IonGLYCEROL
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2FFQ4Ligand/Ion[(1R)-1-HYDROXYPROPYL]PHOSPHONIC ACID
3GOL4Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:138 , GLU A:142 , HIS A:180 , FFQ A:202BINDING SITE FOR RESIDUE FE2 A 201
02AC2SOFTWAREARG A:97 , TYR A:105 , ASN A:135 , HIS A:138 , GLU A:142 , HIS A:180 , PHE A:182 , FE2 A:201 , HOH A:309 , LYS B:23BINDING SITE FOR RESIDUE FFQ A 202
03AC3SOFTWAREARG A:90 , PHE A:145 , GLY A:169 , GLY B:149 , THR B:168BINDING SITE FOR RESIDUE GOL A 203
04AC4SOFTWAREALA A:114 , PRO A:115 , SER A:116BINDING SITE FOR RESIDUE GOL A 204
05AC5SOFTWAREHIS B:138 , GLU B:142 , HIS B:180 , FFQ B:202BINDING SITE FOR RESIDUE FE2 B 201
06AC6SOFTWARELYS A:23 , ARG B:97 , TYR B:105 , ASN B:135 , HIS B:138 , GLU B:142 , HIS B:180 , FE2 B:201 , HOH B:307 , HOH B:309BINDING SITE FOR RESIDUE FFQ B 202
07AC7SOFTWAREGLY A:149 , THR A:168 , ARG B:90 , PHE B:145 , GLY B:169BINDING SITE FOR RESIDUE GOL B 203
08AC8SOFTWAREHIS C:138 , GLU C:142 , HIS C:180 , FFQ C:202BINDING SITE FOR RESIDUE FE2 C 201
09AC9SOFTWARELYS C:23 , ARG C:97 , TYR C:105 , ASN C:135 , HIS C:138 , GLU C:142 , HIS C:180 , FE2 C:201BINDING SITE FOR RESIDUE FFQ C 202
10BC1SOFTWAREARG C:90 , PHE C:145 , GLU C:148 , GLY C:169 , LYS C:192BINDING SITE FOR RESIDUE GOL C 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J1W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J1W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J1W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J1W)

(-) Exons   (0, 0)

(no "Exon" information available for 4J1W)

(-) 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:194
                                                                                                                                                                                                                                  
               SCOP domains d4j1wa1 A:5-76                                                          d4j1wa2 A:77-198 Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhh..hhhhhh....................eeeee....eeeeeee..........eeeeeee...hhhhh........eeeeeeee..eeeeee....eeeeee....eeee.....eeeee......eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1w A   5 KTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains d4j1wb1 B:5-76                                                          d4j1wb2 B:77-198 Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhh..hhhhhh....................eeeee....eeeeeee..........eeeeeee...hhhhh........eeeeeeee..eeeeee....eeeeee....eeee.....eeeee......eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1w B   5 KTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    


Chain C from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains d4j1wc1 C:5-76                                                          d4j1wc2 C:77-198 Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhh...hhhhh....................eeeee....eeeeeee..........eeeeeee...hhhhh........eeeeeeee..eeeeee....eeeeee....eeee.....eeeee......eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1w C   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, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J1W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J1W)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  4j1w
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  HPPE_STRWE | Q56185
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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 2bno 3scf 3scg 3sch 4j1x

(-) Related Entries Specified in the PDB File

1zz7 FEII HPPE IN COMPLEX WITH SUBSTRATE FORM 1
1zz8 FEII HPPE IN COMPLEX WITH SUBSTRATE FORM 2
3scf FE(II)-HPPE WITH S-HPP AND NO
3scg FE(II)-HPPE WITH R-HPP
4j1x FE(II)-HPPE WITH ALTERNATIVE SUBSTRATE (S)-1-HPP