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(-) Description

Title :  STRUCTURE OF A MUTANT OF P450 ERYK IN COMPLEX WITH ERYTHROMYCIN B.
 
Authors :  L. C. Montemiglio, B. Vallone, C. Savino
Date :  24 Jan 13  (Deposition) - 01 May 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase-Antibiotic Complex, Catalytic Domain, Cytochrome P-450 Enzyme System, Substrate Specificity, Macrolide Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Montemiglio, A. Macone, C. Ardiccioni, G. Avella, B. Vallone, C. Savino
Redirecting P450 Eryk Specificity By Rational Site-Directed Mutagenesis.
Biochemistry V. 52 3678 2013
PubMed-ID: 23597312  |  Reference-DOI: 10.1021/BI400223J

(-) Compounds

Molecule 1 - ERYTHROMYCIN C-12 HYDROXYLASE
    Atcc: 11635
    Chains: A
    EC Number: 1.14.13.154
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28B
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: SACCHAROPOLYSPORA ERYTHRAEA NRRL 2338
    Organism Taxid: 405948
    Synonym: CYTOCHROME P450 113A1, ERYK, CYP113A1, ERYTHROMYCIN D C-12 HYDROXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ERB1Ligand/IonERYTHROMYCIN B
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:87 , HIS A:88 , HIS A:95 , ARG A:99 , PHE A:106 , LEU A:238 , ALA A:241 , GLY A:242 , THR A:245 , THR A:246 , LEU A:249 , MET A:291 , ARG A:293 , SER A:345 , PHE A:346 , GLY A:347 , HIS A:351 , CYS A:353 , GLY A:355 , ALA A:359 , ERB A:413 , HOH A:2067 , HOH A:2213 , HOH A:2289 , HOH A:2328BINDING SITE FOR RESIDUE HEM A 412
2AC2SOFTWAREHIS A:88 , GLU A:89 , PRO A:177 , ILE A:186 , LEU A:190 , ALA A:237 , LEU A:240 , ALA A:241 , THR A:245 , PHE A:288 , GLN A:292 , HEM A:412 , HOH A:2086 , HOH A:2212 , HOH A:2213 , HOH A:2248 , HOH A:2254 , HOH A:2329BINDING SITE FOR RESIDUE ERB A 413

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZKP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:92 -Pro A:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.ERYK_SACEN332-341  1A:346-355

(-) Exons   (0, 0)

(no "Exon" information available for 3ZKP)

(-) 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:391
 aligned with ERYK_SACEN | P48635 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:391
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 
           ERYK_SACEN     7 VPGMADETALLDWLGTMREKQPVWQDRYGVWHVFRHADVQTVLRDTATFSSDPTRVIEGASPTPGMIHEIDPPEHRALRKVVSSAFTPRTISDLEPRIRDVTRSLLADAGESFDLVDVLAFPLPVTIVAELLGLPPMDHEQFGDWSGALVDIQMDDPTDPALAERIADVLNPLTAYLKARCAERRADPGDDLISRLVLAEVDGRALDDEEAANFSTALLLAGHITTTVLLGNIVRTLDEHPAHWDAAAEDPGRIPAIVEEVLRYRPPFPQMQRTTTKATEVAGVPIPADVMVNTWVLSANRDSDAHDDPDRFDPSRKSGGAAQLSFGHGVHFCLGAPLARLENRVALEEIIARFGRLTVDRDDERLRHFEQIVLGTRHLPVLAGSSPRQSA 397
               SCOP domains d3zkpa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.eee.....eee.hhhhhhhhhhh...ee.hhhhhh........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeeee...eee..eee....eeeeehhhhhh.................hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.eee.......ee.......eee.eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zkp A  21 VPGMADETALLDWLGTMREKQPVWQDRYGVWHVFRHADVQTVLRDTATFSSDPTRVIEGASPTPGAIHEIDPPEHRALRKVVSSAFTPRTISDLEPRIRDVTRSLLADAGESFDLVDVLAFPLPVTIVAELLGLPPMDHEQFGDWSGALVDIQMDDPTDPALAERIADVLNPLTAYLKARCAERRADPGDDLISRLVLAEVDGRALDDEEAANFSTALLLAGHITTTVLLGNIVRTLDEHPAHWDAAAEDPGRIPAIVEEVLRYRPPFPQMQRTTTKATEVAGVPIPADVMVNTWVLSANRDSDAHDDPDRFDPSRKSGGAAQLSFGHGVHFCLGAPLARLENRVALEEIIARFGRLTVDRDDERLRHFEQIVLGTRHLPVLAGSSPRQSA 411
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410
   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZKP)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ERYK_SACEN | P48635)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0016709    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
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:0033068    macrolide biosynthetic process    The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
    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.

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  3zkp
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  ERYK_SACEN | P48635
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  1.14.13.154
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERYK_SACEN | P48635: 2jjn 2jjo 2jjp 2wio 2xfh

(-) Related Entries Specified in the PDB File

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