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(-) Description

Title :  CRYSTAL STRUCTURE OF CYP105D6
 
Authors :  L. H. Xu, S. Fushinobu, S. Takamatsu, T. Wakagi, H. Ikeda, H. Shoun
Date :  04 Dec 09  (Deposition) - 07 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  P450, Oxidoreductase, Heme, Monooxygenase, Macrolide, Filipin, Iron, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. H. Xu, S. Fushinobu, S. Takamatsu, T. Wakagi, H. Ikeda, H. Shoun
Regio- And Stereospecificity Of Filipin Hydroxylation Sites Revealed By Crystal Structures Of Cytochrome P450 105P1 And 105D6 From Streptomyces Avermitilis
J. Biol. Chem. V. 285 16844 2010
PubMed-ID: 20375018  |  Reference-DOI: 10.1074/JBC.M109.092460
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME P450 HYDROXYLASE
    Chains: A
    EC Number: 1.14.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PTED, SAV412, SAV_412
    Organism Scientific: STREPTOMYCES AVERMITILIS
    Organism Taxid: 33903
    Strain: MA-4680
    Synonym: CYP105D6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:94 , ILE A:95 , HIS A:102 , ARG A:106 , ILE A:158 , LEU A:161 , LEU A:240 , ALA A:243 , GLY A:244 , THR A:247 , THR A:248 , ALA A:251 , SER A:290 , ILE A:293 , ARG A:295 , ILE A:318 , GLY A:345 , PHE A:346 , GLY A:347 , HIS A:351 , CYS A:353 , GLY A:355 , ALA A:359 , HOH A:409 , HOH A:565 , HOH A:595 , HOH A:623BINDING SITE FOR RESIDUE HEM A 1430

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:16 -Pro A:17
2Asp A:99 -Pro A:100
3Pro A:141 -Gly A:142
4Glu A:225 -Gly A:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ABB)

(-) 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:383
 aligned with Q79ZT5_STRAW | Q79ZT5 from UniProtKB/TrEMBL  Length:404

    Alignment length:398
                                                                                                                                                                                                                                                                                                                                                                                                                                   404    
                                    20        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   |    
         Q79ZT5_STRAW    11 SPAPSFPQDRTCPYQPPKAYEERRGESPLTQVTLFDGRPAWLITGHAEGRALLVDPRLSSDWGHPDFPVVVRRTEDRGGLAFPLIGVDDPVHARQRRMLIPSFGVKRMNAIRPRLQSLVDRLLDDMLAKGPGADLVSAFALPVPSVAICELLGVPYGDHDFFEECSRNFVGAATSAEADAAFGELYTYLHGLVGRKQAEPEDGLLDELIARQLEEGDLDHDEVVMIALVLLVAGHETTVNAIALGALTLIQHPEQIDVLLRDPGAVSGVVEELLRFTSVSDHIVRMAKEDIEVGGATIKAGDAVLVSITLMNRDAKAYENPDIFDARRNARHHVGFGHGIHQCLGQNLARAELEIALGGLFARIPGLRLAVPLDEVPIKAGHDAQGPIELPVVW----   -
               SCOP domains d3abba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3abbA00 A:11-408 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhh....eeeee.....eeeee.hhhhhhhhhh...ee............---------.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh------...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhhh........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3abb A  11 SPAPSFPQDRTCPYQPPKAYEERRGESPLTQVTLFDGRPAWLITGHAEGRALLVDPRLSSDWGHPDFPVVV---------AFPLIGVDDPVHARQRRMLIPSFGVKRMNAIRPRLQSLVDRLLDDMLAKGPGADLVSAFALPVPSVAICELLGVPYGDHDFFEECSRNFV------EADAAFGELYTYLHGLVGRKQAEPEDGLLDELIARQLEEGDLDHDEVVMIALVLLVAGHETTVNAIALGALTLIQHPEQIDVLLRDPGAVSGVVEELLRFTSVSDHIVRMAKEDIEVGGATIKAGDAVLVSITLMNRDAKAYENPDIFDARRNARHHVGFGHGIHQCLGQNLARAELEIALGGLFARIPGLRLAVPLDEVPIKAGHDAQGPIELPVVWHHHH 408
                                    20        30        40        50        60        70        80|        -|      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        
                                                                                                 81        91                                                                                      180    187                                                                                                                                                                                                                             


Chain A from PDB  Type:PROTEIN  Length:383
 aligned with Q93H80_STRAX | Q93H80 from UniProtKB/TrEMBL  Length:416

    Alignment length:398
                                                                                                                                                                                                                                                                                                                                                                                                                                   416    
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412   |    
         Q93H80_STRAX    23 SPAPSFPQDRTCPYQPPKAYEERRGESPLTQVTLFDGRPAWLITGHAEGRALLVDPRLSSDWGHPDFPVVVRRTEDRGGLAFPLIGVDDPVHARQRRMLIPSFGVKRMNAIRPRLQSLVDRLLDDMLAKGPGADLVSAFALPVPSVAICELLGVPYGDHDFFEECSRNFVGAATSAEADAAFGELYTYLHGLVGRKQAEPEDGLLDELIARQLEEGDLDHDEVVMIALVLLVAGHETTVNAIALGALTLIQHPEQIDVLLRDPGAVSGVVEELLRFTSVSDHIVRMAKEDIEVGGATIKAGDAVLVSITLMNRDAKAYENPDIFDARRNARHHVGFGHGIHQCLGQNLARAELEIALGGLFARIPGLRLAVPLDEVPIKAGHDAQGPIELPVVW----   -
               SCOP domains d3abba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3abbA00 A:11-408 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhh....eeeee.....eeeee.hhhhhhhhhh...ee............---------.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh------...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhhh........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3abb A  11 SPAPSFPQDRTCPYQPPKAYEERRGESPLTQVTLFDGRPAWLITGHAEGRALLVDPRLSSDWGHPDFPVVV---------AFPLIGVDDPVHARQRRMLIPSFGVKRMNAIRPRLQSLVDRLLDDMLAKGPGADLVSAFALPVPSVAICELLGVPYGDHDFFEECSRNFV------EADAAFGELYTYLHGLVGRKQAEPEDGLLDELIARQLEEGDLDHDEVVMIALVLLVAGHETTVNAIALGALTLIQHPEQIDVLLRDPGAVSGVVEELLRFTSVSDHIVRMAKEDIEVGGATIKAGDAVLVSITLMNRDAKAYENPDIFDARRNARHHVGFGHGIHQCLGQNLARAELEIALGGLFARIPGLRLAVPLDEVPIKAGHDAQGPIELPVVWHHHH 408
                                    20        30        40        50        60        70        80|        -|      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        
                                                                                                 81        91                                                                                      180    187
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q93H80_STRAX | Q93H80)
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: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.

Chain A   (Q79ZT5_STRAW | Q79ZT5)
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: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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 Related Entries

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(-) Related Entries Specified in the PDB File

3aba CYP105P1 IN COMPLEX WITH FILIPIN I