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(-) Description

Title :  CRYSTAL STRUCTURE OF FE(II)-HPPE WITH ALTERNATIVE SUBSTRATE (S)-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 :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C  (4x)
Keywords :  Keto Product, Hydroxypropylphosphonic Acid Epoxidase, 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 2-198)
    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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
11JJ3Ligand/Ion[(1S)-1-HYDROXYPROPYL]PHOSPHONIC ACID
2FE23Ligand/IonFE (II) ION
3GOL1Ligand/IonGLYCEROL
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
11JJ4Ligand/Ion[(1S)-1-HYDROXYPROPYL]PHOSPHONIC ACID
2FE24Ligand/IonFE (II) ION
3GOL2Ligand/IonGLYCEROL
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
11JJ4Ligand/Ion[(1S)-1-HYDROXYPROPYL]PHOSPHONIC ACID
2FE24Ligand/IonFE (II) ION
3GOL-1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:138 , GLU A:142 , HIS A:180 , 1JJ A:202 , HOH A:303BINDING SITE FOR RESIDUE FE2 A 201
2AC2SOFTWAREARG A:97 , TYR A:103 , TYR A:105 , ASN A:135 , HIS A:138 , GLU A:142 , HIS A:180 , PHE A:182 , FE2 A:201 , HOH A:305 , LYS B:23BINDING SITE FOR RESIDUE 1JJ A 202
3AC3SOFTWAREARG A:113 , ALA A:114 , PRO A:115 , SER A:116BINDING SITE FOR RESIDUE GOL A 203
4AC4SOFTWAREHIS B:138 , GLU B:142 , HIS B:180 , 1JJ B:202BINDING SITE FOR RESIDUE FE2 B 201
5AC5SOFTWARELYS A:23 , ARG B:97 , TYR B:103 , TYR B:105 , ASN B:135 , HIS B:138 , GLU B:142 , HIS B:180 , PHE B:182 , LEU B:193 , FE2 B:201 , HOH B:302BINDING SITE FOR RESIDUE 1JJ B 202
6AC6SOFTWAREHIS C:138 , GLU C:142 , HIS C:180 , 1JJ C:202BINDING SITE FOR RESIDUE FE2 C 201
7AC7SOFTWARELYS C:23 , ARG C:97 , TYR C:103 , TYR C:105 , ASN C:135 , HIS C:138 , GLU C:142 , HIS C:180 , FE2 C:201BINDING SITE FOR RESIDUE 1JJ C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J1X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J1X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J1X)

(-) Exons   (0, 0)

(no "Exon" information available for 4J1X)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains d4j1xa1 A:6-76                                                         d4j1xa2 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..............hhhhh.eeeeee..eeeeeeee..........eeeeeee...hhhhh.........eeeeeee..eeeeee....eeeeee....eeee.....eeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1x A   6 TASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195   


Chain B from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains d4j1xb1 B:6-76                                                         d4j1xb2 B:77-198 Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhh..hhhhhh..............hhhhh.eeeeee..eeeeeeee..........eeeeeee...hhhhh.........eeeeeee..eeeeee....eeeeee....eeee.....eeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1x B   6 TASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195   


Chain C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains d4j1xc1 C:4-76                                                           d4j1xc2 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..hhhhhh..............hhhhh.eeeeee..eeeeeeee..........eeeeeee...hhhhh.........eeeeeee..eeeeee....eeeeee....eeee.....eeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1x C   4 TKTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSLVPLVVDVLTDNPDDAKFNSGHAGNEFLFVLEGEIHMKWGDKENPKEALLPTGASMFVEEHVPHAFTAAKGTGSAKLIAVNF 198
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
   Legend:   → Mismatch (orange background)
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    → 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 4J1X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J1X)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  4j1x
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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 4j1w

(-) Related Entries Specified in the PDB File

1zz7 FE(II)-HPPE WITH SUBSTRATE FORM 1
1zz8 FE(II)-HPPE WITH SUBSTRATE FORM 2
3scf FE(II)-HPPE WITH S-HPP AND NO
3scg FE(II)-HPPE WITH R-HPP
4j1w FE(II)-HPPE WITH ALTERNATIVE SUBSTRATES (R)-1-HPP AND (S)- 1-HPP