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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SUBSTRATE-FREE CYP109E1 FROM BACILLUS MEGATERIUM AT 2.55 ANGSTROM RESOLUTION
 
Authors :  I. K. Jozwik, A. M. W. H. Thunnissen
Date :  09 Jun 16  (Deposition) - 05 Oct 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bacillus, Bacterial Proteins, Binding Sites, Catalysis, Cytochrome P- 450 Enzyme System, Cytochrome P450, Hydroxylation, Escherichia Coli, Heme, Ligands, Molecular Structure, Oxidation-Reduction, Oxygen, Protein, Protein Structure, Secondary, Steroids, Substrate Specificity, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. K. Jozwik, F. M. Kiss, A. Abdulmughni, E. Brill, J. Zapp, J. Pleiss, R. Bernhardt, A. W. Thunnissen
Structural Basis Of Steroid Binding And Oxidation By The Cytochrome P450 Cyp109E1 From Bacillus Megaterium.
Febs J. V. 283 4128 2016
PubMed-ID: 27686671  |  Reference-DOI: 10.1111/FEBS.13911

(-) Compounds

Molecule 1 - CYTOCHROME P450
    Chains: A, B
    EC Number: 1.14.14.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C43
    Gene: BMD_3874
    Organism Scientific: BACILLUS MEGATERIUM (STRAIN DSM 319)
    Organism Taxid: 592022
    Strain: DSM 319

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:84 , ILE A:85 , HIS A:92 , ARG A:96 , LEU A:239 , ALA A:242 , GLY A:243 , THR A:246 , THR A:247 , LEU A:292 , ARG A:294 , ALA A:344 , PHE A:345 , GLY A:346 , HIS A:350 , CYS A:352 , GLY A:354 , ALA A:358 , HOH A:601binding site for residue HEM A 501
2AC2SOFTWARELEU B:84 , ILE B:85 , HIS B:92 , ARG B:96 , ILE B:147 , LEU B:239 , ALA B:242 , GLY B:243 , THR B:246 , THR B:247 , LEU B:292 , ARG B:294 , MET B:317 , ALA B:344 , PHE B:345 , GLY B:346 , ILE B:349 , HIS B:350 , CYS B:352 , GLY B:354 , ALA B:358binding site for residue HEM B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L90)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:89 -Pro A:90
2Lys A:338 -Pro A:339
3Pro B:89 -Pro B:90
4Lys B:338 -Pro B:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L90)

(-) Exons   (0, 0)

(no "Exon" information available for 5L90)

(-) 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:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...eeee....eeee.hhhhhhhhhhh...ee............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee......ee........eee.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l90 A  21 ERFNPFSWYEEMRNTAPVQWDEERQVWDVFHYDGVKEVLEQKNIFSSDRRPPQNQRQTALGTSLINIDPPKHAEMRALVNKAFTPKAMKAWEPKIARITNELLQEVEHLEDIDIVEHLSYPLPVMVIADILGVPIEDQRQFKDWSDIIVAGPSNNERETLEKLQQEKMKANDELETYFYRIIEEKRTRPGDDIISVLLQAKEEGKQLTDEEIVGFSILLLIAGNETTTNLISNTIYCLMEDKASFERLKREKELLPSGIEEVLRYRSPVQALHRIVKEDVTLAGKKLKAGEHVVPWMGSAHRDAEYFEDPEVFKIDRKPNVHMAFGRGIHFCLGAPLARIEAKIMLAELIDRYPQMDWSPSFELKPIESTFVYGLKELLIRKNVH 405
                                    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     


Chain B from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeee....eeee.hhhhhhhhhhh...ee...........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee....................eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l90 B  21 ERFNPFSWYEEMRNTAPVQWDEERQVWDVFHYDGVKEVLEQKNIFSSDRRPPQNQRQTALGTSLINIDPPKHAEMRALVNKAFTPKAMKAWEPKIARITNELLQEVEHLEDIDIVEHLSYPLPVMVIADILGVPIEDQRQFKDWSDIIVAGPSNNERETLEKLQQEKMKANDELETYFYRIIEEKRTRPGDDIISVLLQAKEEGKQLTDEEIVGFSILLLIAGNETTTNLISNTIYCLMEDKASFERLKREKELLPSGIEEVLRYRSPVQALHRIVKEDVTLAGKKLKAGEHVVPWMGSAHRDAEYFEDPEVFKIDRKPNVHMAFGRGIHFCLGAPLARIEAKIMLAELIDRYPQMDWSPSFELKPIESTFVYGLKELLIRKNVH 405
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 5L90)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L90)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L90)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  5l90
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 Related Entries

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        D5DKI8_BACMD | D5DKI8: 5l91 5l92 5l94

(-) Related Entries Specified in the PDB File

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