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(-) Description

Title :  STRUCTURE OF CYTOCHROME P450 ERYK IN COMPLEX WITH ITS NATURAL SUBSTRATE ERD
 
Authors :  C. Savino, G. Sciara, A. E. Miele, S. G. Kendrew, B. Vallone
Date :  15 Apr 08  (Deposition) - 14 Jul 09  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A
Keywords :  Iron, Heme, Monooxygenase, Metal-Binding, Antibiotic Biosynthesis, Tie-Rod Mechanism Of Action, Oxidoreductase, Substrate Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Savino, L. C. Montemiglio, G. Sciara, A. E. Miele, S. G. Kendrew, P. Jemth, S. Gianni, B. Vallone
Investigating The Structural Plasticity Of A Cytochrome P450: Three-Dimensional Structures Of P450 Eryk And Binding To Its Physiological Substrate.
J. Biol. Chem. V. 284 29170 2009
PubMed-ID: 19625248  |  Reference-DOI: 10.1074/JBC.M109.003590

(-) Compounds

Molecule 1 - CYTOCHROME P450 113A1
    Chains: A
    EC Number: 1.14.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21STAR
    Expression System Taxid: 511693
    Expression System Vector: PET28B
    Mutation: YES
    Organism Scientific: SACCHAROPOLYSPORA ERYTHRAEA
    Organism Taxid: 1836
    Other Details: CDNA
    Strain: NRRL 23338
    Synonym: CYTOCROME P450 CYP113A1, ERYTHROMYCIN B/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
1EY51Ligand/IonERYTHROMYCIN D
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 , EY5 A:413 , HOH A:2080 , HOH A:2331 , HOH A:2332 , HOH A:2333BINDING SITE FOR RESIDUE HEM A 412
2AC2SOFTWAREHIS A:88 , GLU A:89 , LEU A:169 , ILE A:172 , MET A:174 , PRO A:177 , ILE A:186 , LEU A:240 , ALA A:241 , THR A:245 , PHE A:288 , GLN A:292 , HEM A:412 , HOH A:2217 , HOH A:2238 , HOH A:2332 , HOH A:2334 , HOH A:2335BINDING SITE FOR RESIDUE EY5 A 413

(-) SS Bonds  (0, 0)

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

(-) 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 2JJO)

(-) 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 2JJO)

(-) 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:393
 aligned with ERYK_SACEN | P48635 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:393
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394   
           ERYK_SACEN     5 DEVPGMADETALLDWLGTMREKQPVWQDRYGVWHVFRHADVQTVLRDTATFSSDPTRVIEGASPTPGMIHEIDPPEHRALRKVVSSAFTPRTISDLEPRIRDVTRSLLADAGESFDLVDVLAFPLPVTIVAELLGLPPMDHEQFGDWSGALVDIQMDDPTDPALAERIADVLNPLTAYLKARCAERRADPGDDLISRLVLAEVDGRALDDEEAANFSTALLLAGHITTTVLLGNIVRTLDEHPAHWDAAAEDPGRIPAIVEEVLRYRPPFPQMQRTTTKATEVAGVPIPADVMVNTWVLSANRDSDAHDDPDRFDPSRKSGGAAQLSFGHGVHFCLGAPLARLENRVALEEIIARFGRLTVDRDDERLRHFEQIVLGTRHLPVLAGSSPRQSA 397
               SCOP domains d2jjoa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh.eee.....eee.hhhhhhhhhhh...ee.hhhhhh........hhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeehhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeeee...eee..eee....eeeeehhhhhh.................hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.eee....................eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jjo A  19 DEVPGMADETALLDWLGTMREKQPVWQDRYGVWHVFRHADVQTVLRDTATFSSDPTRVIEGASPTPGMIHEIDPPEHRALRKVVSSAFTPRTISDLEPRIRDVTRSLLADAGESFDLVDVLAFPLPVTIVAELLGLPPMDHEQFGDWSGALVDIQMDDPTDPALAERIADVLNPLTAYLKARCAERRADPGDDLISRLVLAEVDGRALDDEEAANFSTALLLAGHITTTVLLGNIVRTLDEHPAHWDAAAEDPGRIPAIVEEVLRYRPPFPQMQRTTTKATEVAGVPIPADVMVNTWVLSANRDSDAHDDPDRFDPSRKSGGAAQLSFGHGVHFCLGAPLARLENRVALEEIIARFGRLTVDRDDERLRHFEQIVLGTRHLPVLAGSSPRQSA 411
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  2jjo
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  ERYK_SACEN | P48635
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERYK_SACEN | P48635: 2jjn 2jjp 2wio 2xfh 3zkp

(-) Related Entries Specified in the PDB File

2jjn STRUCTURE OF CLOSED CYTOCHROME P450 ERYK
2jjp STRUCTURE OF CYTOCHROME P450 ERYK IN COMPLEX WITH INHIBITOR KETOCONAZOLE (KC)
2vru STRUCTURE OF OPEN HISTIDINE TAGGED CYTOCHROME P450 ERYK
2vrv STRUCTURE OF HISTIDINE TAGGED CYTOCHROME P450 ERYK IN COMPLEX WITH INHIBITOR CLOTRIMAZOLE (CLT)
2wio STRUCTURE OF THE OPEN HISTIDINE TAGGED C. SAVINO, CYTOCHROME P450 ERYK