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(-) Description

Title :  STRUCTURE OF CYTOCHROME P450 VDH FROM PSEUDONOCARDIA AUTOTROPHICA (TRIGONAL CRYSTAL FORM)
 
Authors :  Y. Yasutake, Y. Fujii, W. K. Cheon, A. Arisawa, T. Tamura
Date :  07 Jul 09  (Deposition) - 14 Jul 10  (Release) - 17 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450, Vitamin D3 Hydroxylase, Hemoprotein, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yasutake, Y. Fujii, T. Nishioka, W. K. Cheon, A. Arisawa, T. Tamura
Structural Evidence For Enhancement Of Sequential Vitamin D Hydroxylation Activities By Directed Evolution Of Cytochrom P450 Vitamin D3 Hydroxylase
J. Biol. Chem. V. 285 31193 2010
PubMed-ID: 20667833  |  Reference-DOI: 10.1074/JBC.M110.147009

(-) Compounds

Molecule 1 - VITAMIN D HYDROXYLASE
    Chains: A
    Engineered: YES
    Expression System: RHODOCOCCUS ERYTHROPOLIS
    Expression System Plasmid: PTIP-QC2
    Expression System Strain: L88
    Expression System Taxid: 1833
    Expression System Vector Type: PLASMID
    Gene: VDH
    Organism Scientific: PSEUDONOCARDIA AUTOTROPHICA
    Organism Taxid: 2074
    Strain: NBRC 12743

 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
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:58 , LYS A:65 , MET A:87 , ILE A:88 , HIS A:95 , ARG A:99 , ALA A:236 , GLY A:237 , THR A:240 , THR A:241 , PRO A:287 , ARG A:289 , LEU A:312 , PHE A:339 , PHE A:340 , GLY A:341 , ILE A:344 , HIS A:345 , CYS A:347 , GLY A:349 , ALA A:353 , PG0 A:420 , HOH A:508 , HOH A:763BINDING SITE FOR RESIDUE HEM A 412
2AC2SOFTWAREILE A:88 , LEU A:232 , HEM A:412 , HOH A:622 , HOH A:763BINDING SITE FOR RESIDUE PG0 A 420

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A4G)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:92 -Pro A:93
2Gly A:133 -Pro A:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A4G)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CPVDH_PSEAH340-349  1A:340-349

(-) Exons   (0, 0)

(no "Exon" information available for 3A4G)

(-) 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:395
 aligned with CPVDH_PSEAH | C4B644 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:395
                                    18        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     
          CPVDH_PSEAH     9 EQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRYADVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKLVGRSFTVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVICELLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTEPDDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLALLTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVTIPAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCLGAQLARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPRSA 403
               SCOP domains d3a4ga_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..hhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...ee.hhhhhhhhhhh.........hhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....eehhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh........eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a4g A   9 EQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRYADVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKLVGRSFTVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVICELLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTEPDDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLALLTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVTIPAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCLGAQLARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPRSA 403
                                    18        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
   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 3A4G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A4G)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CPVDH_PSEAH | C4B644)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3a4g
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 Related Entries

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

UniProtKB/Swiss-Prot
        CPVDH_PSEAH | C4B644: 3a4h 3a4z 3a50 3a51 3vrm 5gnl 5gnm

(-) Related Entries Specified in the PDB File

3a4h 3a4z 3a50 3a51