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(-) Description

Title :  CRYSTAL STRUCTURE OF CAMPHOR-BOUND CYP101D2
 
Authors :  W. Yang, S. G. Bell, H. Wang, W. H. Zhou, M. Bartlam, L. L. Wong, Z. Rao
Date :  08 Jul 10  (Deposition) - 03 Nov 10  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450 Fold, Oxidizing Camphor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Yang, S. G. Bell, H. Wang, W. Zhou, M. Bartlam, L. L. Wong, Z. Rao
The Structure Of Cyp101D2 Unveils A Potential Path For Substrate Entry Into The Active Site
Biochem. J. V. 433 85 2011
PubMed-ID: 20950270  |  Reference-DOI: 10.1042/BJ20101017

(-) Compounds

Molecule 1 - CYTOCHROME P450
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SARO_1478
    Organism Scientific: NOVOSPHINGOBIUM AROMATICIVORANS
    Organism Taxid: 279238
    Strain: DSM 12444
    Synonym: CYP101D2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CAM1Ligand/IonCAMPHOR
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:102 , HIS A:109 , ARG A:113 , LEU A:251 , LEU A:252 , GLY A:255 , GLY A:256 , THR A:259 , GLU A:304 , ARG A:306 , THR A:356 , PHE A:357 , GLY A:358 , HIS A:362 , CYS A:364 , GLY A:366 , CAM A:422 , HOH A:464 , HOH A:498 , HOH A:589BINDING SITE FOR RESIDUE HEM A 418
2AC2SOFTWAREGLY A:255 , ILE A:402 , VAL A:403 , HEM A:418 , HOH A:589BINDING SITE FOR RESIDUE CAM A 422
3AC3SOFTWAREALA A:202 , GLY A:206 , HIS A:270 , HIS A:274 , LEU A:277 , TRP A:343 , LYS A:344 , LEU A:345 , HOH A:489 , HOH A:667 , HOH A:708 , HOH A:736BINDING SITE FOR RESIDUE PEG A 747

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NV6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:89 -Pro A:90
2Val A:100 -Pro A:101
3Pro A:106 -Pro A:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NV6)

(-) Exons   (0, 0)

(no "Exon" information available for 3NV6)

(-) 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:404
 aligned with Q2G8A2_NOVAD | Q2G8A2 from UniProtKB/TrEMBL  Length:417

    Alignment length: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       410    
         Q2G8A2_NOVAD    11 AKVERPANVPEDRVYEIDMYALNGIEDGYHEAWKKVQHPGIPDLIWTPFTGGHWIATNGDTVKEVYSDPTRFSSEVIFLPKEAGEKYQMVPTKMDPPEHTPYRKALDKGLNLAKIRKVEDKVREVASSLIDSFAARGECDFAAEYAELFPVHVFMALADLPLEDIPVLSEYARQMTRPEGNTPEEMATDLEAGNNGFYAYVDPIIRARVGGDGDDLITLMVNSEINGERIAHDKAQGLISLLLLGGLDTVVNFLSFFMIHLARHPELVAELRSDPLKLMRGAEEMFRRFPVVSEARMVAKDQEYKGVFLKRGDMILLPTALHGLDDAANPEPWKLDFSRRSISHSTFGGGPHRCAGMHLARMEVIVTLEEWLKRIPEFSFKEGETPIYHSGIVAAVENVPLVWP 414
               SCOP domains d3nv6a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-3nv6A01 A:221-404                                                                                                                                                                  ---------- Pfam domains
         Sec.struct. author .........hhhhh.........hhhhhhhhhhhhhh......eeee.....eeee.hhhhhhhhhhh...ee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhhh........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee......eee.....eee..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nv6 A  11 AKVERPANVPEDRVYEIDMYALNGIEDGYHEAWKKVQHPGIPDLIWTPFTGGHWIATNGDTVKEVYSDPTRFSSEVIFLPKEAGEKYQMVPTKMDPPEHTPYRKALDKGLNLAKIRKVEDKVREVASSLIDSFAARGECDFAAEYAELFPVHVFMALADLPLEDIPVLSEYARQMTRPEGNTPEEMATDLEAGNNGFYAYVDPIIRARVGGDGDDLITLMVNSEINGERIAHDKAQGLISLLLLGGLDTVVNFLSFFMIHLARHPELVAELRSDPLKLMRGAEEMFRRFPVVSEARMVAKDQEYKGVFLKRGDMILLPTALHGLDDAANPEPWKLDFSRRSISHSTFGGGPHRCAGMHLARMEVIVTLEEWLKRIPEFSFKEGETPIYHSGIVAAVENVPLVWP 414
                                    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       410
   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 3NV6)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: p450] (161)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q2G8A2_NOVAD | Q2G8A2)
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

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

UniProtKB/TrEMBL
        Q2G8A2_NOVAD | Q2G8A2: 3nv5 4dxy

(-) Related Entries Specified in the PDB File

3nv5 CRYSTAL STRUCTURE OF CYTOCHROME P450 CYP101D2