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(-) Description

Title :  CRYSTAL STRUCTURE OF P450 OXYD THAT IS INVOLVED IN THE BIOSYNTHESIS OF VANCOMYCIN-TYPE ANTIBIOTICS
 
Authors :  M. J. Cryle, I. Schlichting
Date :  07 Apr 10  (Deposition) - 02 Jun 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytochrome P450 Oxidase, Haem Protein, Vancomycin Biosynthesis, Carrier Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Cryle, A. Meinhart, I. Schlichting
Structural Characterization Of Oxyd, A Cytochrome P450 Involved In {Beta}-Hydroxytyrosine Formation In Vancomycin Biosynthesis
J. Biol. Chem. V. 285 24562 2010
PubMed-ID: 20519494  |  Reference-DOI: 10.1074/JBC.M110.131904

(-) Compounds

Molecule 1 - PUTATIVE P450 MONOOXYGENASE
    Chains: A, B
    EC Number: 1.14.14.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OXYD
    Organism Scientific: AMYCOLATOPSIS BALHIMYCINA
    Organism Taxid: 208443
    Strain: DSM 5908
    Synonym: CYTOCHROME P450 OXYD (CYP146)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:70 , MET A:87 , VAL A:88 , HIS A:95 , ARG A:99 , GLY A:235 , GLY A:236 , THR A:239 , THR A:240 , LEU A:276 , VAL A:285 , ARG A:287 , THR A:337 , PHE A:338 , GLY A:339 , HIS A:343 , CYS A:345 , GLY A:347 , GOL A:399 , HOH A:432 , HOH A:448 , HOH A:459BINDING SITE FOR RESIDUE HEM A 397
02AC2SOFTWAREGLU A:19 , HOH A:439 , HOH A:468 , HOH A:469 , LEU B:18 , HIS B:21 , HIS B:249 , TRP B:278 , ARG B:315BINDING SITE FOR RESIDUE GOL A 398
03AC3SOFTWAREMET A:70 , ASN A:231 , GLY A:235 , HEM A:397 , GOL A:400 , HOH A:448BINDING SITE FOR RESIDUE GOL A 399
04AC4SOFTWAREMET A:70 , MET A:71 , ASP A:80 , VAL A:88 , GOL A:399 , HOH A:460BINDING SITE FOR RESIDUE GOL A 400
05AC5SOFTWARELEU A:18 , HIS A:249 , TRP A:278 , ARG A:315 , TRP A:377 , GLU B:19BINDING SITE FOR RESIDUE GOL A 401
06AC6SOFTWAREARG A:99 , HIS A:344 , CYS A:345 , LEU A:346 , SER A:348 , HOH A:416BINDING SITE FOR RESIDUE GOL A 402
07AC7SOFTWAREMET B:70 , MET B:87 , VAL B:88 , HIS B:95 , ARG B:99 , GLY B:235 , GLY B:236 , THR B:239 , THR B:240 , LEU B:276 , VAL B:285 , ARG B:287 , THR B:337 , PHE B:338 , GLY B:339 , HIS B:343 , CYS B:345 , GLY B:347 , GOL B:399 , HOH B:440 , HOH B:448 , HOH B:498BINDING SITE FOR RESIDUE HEM B 397
08AC8SOFTWAREMET B:71 , ASP B:80 , ILE B:234 , GOL B:399 , HOH B:406 , HOH B:429 , HOH B:506BINDING SITE FOR RESIDUE GOL B 398
09AC9SOFTWAREMET B:71 , ASN B:231 , ILE B:234 , GLY B:235 , HEM B:397 , GOL B:398 , HOH B:435 , HOH B:498 , HOH B:529BINDING SITE FOR RESIDUE GOL B 399
10BC1SOFTWAREALA B:6 , VAL B:7 , ASP B:8BINDING SITE FOR RESIDUE GOL B 400
11BC2SOFTWAREASP B:269 , ARG B:352 , HOH B:449BINDING SITE FOR RESIDUE GOL B 401
12BC3SOFTWAREMET B:33 , HOH B:465 , HOH B:538BINDING SITE FOR RESIDUE GOL B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:133 -Val A:134
2Lys A:331 -Pro A:332
3Lys B:331 -Pro B:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MGX)

(-) Exons   (0, 0)

(no "Exon" information available for 3MGX)

(-) 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:387
 aligned with Q939Y1_AMYBA | Q939Y1 from UniProtKB/TrEMBL  Length:396

    Alignment length:391
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395 
         Q939Y1_AMYBA     6 AVDLGNPDLYTTLERHARWRELAAEDAMVWSDPGSSPSGFWSVFSHRACAAVLAPSAPLTSEYGMMIGFDRDHPDNSGGRMMVVSEHEQHRKLRKLVGPLLSRAAARKLAERVRIEVGDVLGRVLDGEVCDAATAIGPRIPAAVVCEILGVPAEDEDMLIDLTNHAFGGEDELFDGMTPRQAHTEILVYFDELITARRKEPGDDLVSTLVTDDDLTIDDVLLNCDNVLIGGNETTRHAITGAVHALATVPGLLTALRDGSADVDTVVEEVLRWTSPAMHVLRVTTADVTINGRDLPSGTPVVAWLPAANRDPAEFDDPDTFLPGRKPNRHITFGHGMHHCLGSALARIELSVVLRVLAERVSRVDLEREPAWLRAIVVQGYRELPVRFTGR 396
               SCOP domains d3mgxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh..eee........eeee.hhhhhhhhh.....ee....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....----..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhheeeeee....ee........eee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mgx A   6 AVDLGNPDLYTTLERHARWRELAAEDAMVWSDPGSSPSGFWSVFSHRACAAVLAPSAPLTSEYGMMIGFDRDHPDNSGGRMMVVSEHEQHRKLRKLVGPLLSRAAARKLAERVRIEVGDVLGRVLDGEVCDAATAIGPRIPAAVVCEILGVPAEDEDMLIDLTNHAFGGED----GMTPRQAHTEILVYFDELITARRKEPGDDLVSTLVTDDDLTIDDVLLNCDNVLIGGNETTRHAITGAVHALATVPGLLTALRDGSADVDTVVEEVLRWTSPAMHVLRVTTADVTINGRDLPSGTPVVAWLPAANRDPAEFDDPDTFLPGRKPNRHITFGHGMHHCLGSALARIELSVVLRVLAERVSRVDLEREPAWLRAIVVQGYRELPVRFTGR 396
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175|    | 185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395 
                                                                                                                                                                                                    176  181                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:391
 aligned with Q939Y1_AMYBA | Q939Y1 from UniProtKB/TrEMBL  Length:396

    Alignment length:391
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395 
         Q939Y1_AMYBA     6 AVDLGNPDLYTTLERHARWRELAAEDAMVWSDPGSSPSGFWSVFSHRACAAVLAPSAPLTSEYGMMIGFDRDHPDNSGGRMMVVSEHEQHRKLRKLVGPLLSRAAARKLAERVRIEVGDVLGRVLDGEVCDAATAIGPRIPAAVVCEILGVPAEDEDMLIDLTNHAFGGEDELFDGMTPRQAHTEILVYFDELITARRKEPGDDLVSTLVTDDDLTIDDVLLNCDNVLIGGNETTRHAITGAVHALATVPGLLTALRDGSADVDTVVEEVLRWTSPAMHVLRVTTADVTINGRDLPSGTPVVAWLPAANRDPAEFDDPDTFLPGRKPNRHITFGHGMHHCLGSALARIELSVVLRVLAERVSRVDLEREPAWLRAIVVQGYRELPVRFTGR 396
               SCOP domains d3mgxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh...hhhhhhhhhhhh..eeee........eeee.hhhhhhhhh.....ee....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh....eeeee...eee..eee....eeeehhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhheeeeee....ee........eee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mgx B   6 AVDLGNPDLYTTLERHARWRELAAEDAMVWSDPGSSPSGFWSVFSHRACAAVLAPSAPLTSEYGMMIGFDRDHPDNSGGRMMVVSEHEQHRKLRKLVGPLLSRAAARKLAERVRIEVGDVLGRVLDGEVCDAATAIGPRIPAAVVCEILGVPAEDEDMLIDLTNHAFGGEDELFDGMTPRQAHTEILVYFDELITARRKEPGDDLVSTLVTDDDLTIDDVLLNCDNVLIGGNETTRHAITGAVHALATVPGLLTALRDGSADVDTVVEEVLRWTSPAMHVLRVTTADVTINGRDLPSGTPVVAWLPAANRDPAEFDDPDTFLPGRKPNRHITFGHGMHHCLGSALARIELSVVLRVLAERVSRVDLEREPAWLRAIVVQGYRELPVRFTGR 396
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q939Y1_AMYBA | Q939Y1)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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: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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