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(-) Description

Title :  MIXED-FUNCTION P450 MYCG IN COMPLEX WITH MYCINAMICIN III IN P21212 SPACE GROUP
 
Authors :  S. Li, P. M. Kells, D. H. Sherman, L. M. Podust
Date :  12 Mar 11  (Deposition) - 28 Mar 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Mycinamicin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Li, D. R. Tietz, F. U. Rutaganira, P. M. Kells, Y. Anzai, F. Kato, T. C. Pochapsky, D. H. Sherman, L. M. Podust
Substrate Recognition By The Multifunctional Cytochrome P450 Mycg In Mycinamicin Hydroxylation And Epoxidation Reactions.
J. Biol. Chem. V. 287 37880 2012
PubMed-ID: 22952225  |  Reference-DOI: 10.1074/JBC.M112.410340

(-) Compounds

Molecule 1 - P-450-LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28B
    Expression System Vector Type: PLASMID
    Organism Scientific: MICROMONOSPORA GRISEORUBIDA
    Organism Taxid: 28040
    Synonym: MYCG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SIN1Ligand/IonSUCCINIC ACID
4ZM31Ligand/IonMYCINAMICIN III

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:84 , HIS A:91 , ARG A:95 , PHE A:102 , ALA A:234 , GLY A:235 , SER A:238 , THR A:239 , PHE A:286 , ARG A:288 , PHE A:339 , GLY A:340 , HIS A:344 , CYS A:346 , LEU A:347 , GLY A:348 , ZM3 A:460 , HOH A:2195 , HOH A:2324BINDING SITE FOR RESIDUE HEM A 450
2AC2SOFTWARELEU A:84 , TYR A:187 , VAL A:233 , ALA A:234 , GLU A:237 , SER A:238 , GLY A:281 , THR A:284 , THR A:311 , HEM A:450 , GOL A:1399 , HOH A:2191 , HOH A:2198 , HOH A:2199 , HOH A:2325BINDING SITE FOR RESIDUE ZM3 A 460
3AC3SOFTWARELEU A:56 , GLY A:57 , ASP A:58 , GLY A:59 , PHE A:61 , PRO A:88 , ASP A:325 , GLY A:342 , VAL A:343 , HOH A:2093 , HOH A:2264 , HOH A:2266BINDING SITE FOR RESIDUE GOL A1398
4AC4SOFTWAREPRO A:72 , ARG A:73 , THR A:284 , PRO A:287 , LEU A:308 , ZM3 A:460 , HOH A:2327BINDING SITE FOR RESIDUE GOL A1399
5AC5SOFTWAREARG A:140 , THR A:240 , ALA A:244 , GLY A:389 , PRO A:390 , LEU A:391 , HOH A:2328BINDING SITE FOR RESIDUE GOL A1400
6AC6SOFTWAREALA A:126 , ARG A:366 , LEU A:367 , TRP A:397 , HOH A:2306BINDING SITE FOR RESIDUE SIN A1401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:9 -Pro A:10
2Pro A:88 -Pro A:89
3Gln A:130 -Pro A:131
4Thr A:332 -Pro A:333

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.MYCG_MICGR339-348  1A:339-348

(-) Exons   (0, 0)

(no "Exon" information available for 2YCA)

(-) 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 MYCG_MICGR | Q59523 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   
           MYCG_MICGR     5 EPRAYPFNDVHGLTLAGRYGELQETEPVSRVRPPYGEEAWLVTRYEDVRAVLGDGRFVRGPSMTRDEPRTRPEMVKGGLLSMDPPEHSRLRRLVVKAFTARRAESLRPRAREIAHELVDQMAATGQPADLVAMFARQLPVRVICELLGVPSADHDRFTRWSGAFLSTAEVTAEEMQEAAEQAYAYMGDLIDRRRKEPTDDLVSALVQARDQQDSLSEQELLDLAIGLLVAGYESTTTQIADFVYLLMTRPELRRQLLDRPELIPSAVEELTRWVPLGVGTAFPRYAVEDVTLRGVTIRAGEPVLASTGAANRDQAQFPDADRIDVDRTPNQHLGFGHGVHHCLGAPLARVELQVALEVLLQRLPGIRLGIPETQLRWSEGMLLRGPLELPVVW 397
               SCOP domains d2ycaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...........hhhhhhhhhhh.eeeee......eeee.hhhhhhhhhhh..eehhhhhh............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........eee...eee..eee....eeeehhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yca A   5 EPRAYPFNDVHGLTLAGRYGELQETEPVSRVRPPYGEEAWLVTRYEDVRAVLGDGRFVRGPSMTRDEPRTRPEMVKGGLLSMDPPEHSRLRRLVVKAFTARRAESLRPRAREIAHELVDQMAATGQPADLVAMFARQLPVRVICELLGVPSADHDRFTRWSGAFLSTAEVTAEEMQEAAEQAYAYMGDLIDRRRKEPTDDLVSALVQARDQQDSLSEQELLDLAIGLLVAGYESTTTQIADFVYLLMTRPELRRQLLDRPELIPSAVEELTRWVPLGVGTAFPRYAVEDVTLRGVTIRAGEPVLASTGAANRDQAQFPDADRIDVDRTPNQHLGFGHGVHHCLGAPLARVELQVALEVLLQRLPGIRLGIPETQLRWSEGMLLRGPLELPVVW 397
                                    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
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MYCG_MICGR | Q59523)
molecular function
    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.
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.

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  2yca
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  MYCG_MICGR | Q59523
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 Related Entries

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

UniProtKB/Swiss-Prot
        MYCG_MICGR | Q59523: 2y46 2y5n 2y5z 2y98 2ygx 3zsn 4aw3

(-) Related Entries Specified in the PDB File

2y46 STRUCTURE OF THE MIXED-FUNCTION P450 MYCG IN COMPLEX WITH MYCINAMICIN IV
2y5n STRUCTURE OF THE MIXED-FUNCTION P450 MYCG IN COMPLEX WITH MYCINAMICIN V IN P21 SPACE GROUP
2y5z STRUCTURE OF THE MIXED-FUNCTION P450 MYCG IN COMPLEX WITH MYCINAMICIN III IN C2221 SPACE GROUP
2y98 STRUCTURE OF THE MIXED-FUNCTION P450 MYCG IN COMPLEX WITH MYCINAMICIN IV IN P21212 SPACE GROUP