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(-) Description

Title :  THE 2.25 A CRYSTAL STRUCTURE OF CYP109E1 FROM BACILLUS MEGATERIUM IN COMPLEX WITH TESTOSTERONE
 
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 :  2.25
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, Testosterone, 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
    Expression System Taxid: 562
    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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2TES1Ligand/IonTESTOSTERONE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2TES1Ligand/IonTESTOSTERONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2TES-1Ligand/IonTESTOSTERONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:84 , ILE A:85 , HIS A:92 , ARG A:96 , ILE A:147 , LEU A:238 , ALA A:242 , THR A:246 , ARG A:294 , ALA A:344 , PHE A:345 , GLY A:346 , HIS A:350 , CYS A:352 , GLY A:354 , ALA A:358 , TES A:502 , HOH A:612 , HOH A:682binding site for residue HEM A 501
2AC2SOFTWAREILE A:241 , VAL A:289 , PHE A:391 , HEM A:501binding site for residue TES A 502
3AC3SOFTWARELEU B:84 , ILE B:85 , HIS B:92 , ARG B:96 , ILE B:147 , ALA B:242 , GLY B:243 , THR B:246 , THR B:247 , LEU B:292 , ARG B:294 , ALA B:344 , PHE B:345 , GLY B:346 , ILE B:349 , HIS B:350 , CYS B:352 , GLY B:354 , ALA B:358 , HOH B:624 , HOH B:638 , HOH B:678binding site for residue HEM B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L94)

(-) 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 5L94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L94)

(-) Exons   (0, 0)

(no "Exon" information available for 5L94)

(-) 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 .hhhhhh.hhhhhhhhhh...eeee....eeee.hhhhhhhhhhh...ee.........hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee....................eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l94 A  17 QTKEERFNPFSWYEEMRNTAPVQWDEERQVWDVFHYDGVKEVLEQKNIFSSDRRPQRQTALGTSLINIDPPKHAEMRALVNKAFTPKAMKAWEPKIARITNELLQEVEHLEDIDIVEHLSYPLPVMVIADILGVPIEDQRQFKDWSDIIVAGPSNNERETLEKLQQEKMKANDELETYFYRIIEEKRTRPGDDIISVLLQAKEEGKQLTDEEIVGFSILLLIAGNETTTNLISNTIYCLMEDKASFERLKREKELLPSGIEEVLRYRSPVQALHRIVKEDVTLAGKKLKAGEHVVPWMGSAHRDAEYFEDPEVFKIDRKPNVHMAFGRGIHFCLGAPLARIEAKIMLAELIDRYPQMDWSPSFELKPIESTFVYGLKELLIRKNV 404
                                    26        36        46        56        66    ||  79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399     
                                                                                 71|                                                                                                                                                                                                                                                                                                                                         
                                                                                  75                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.eeee....eeee.hhhhhhhhhhh...ee....hhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee....................eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l94 B  23 FNPFSWYEEMRNTAPVQWDEERQVWDVFHYDGVKEVLEQKNIFSSDGTSLINIDPPKHAEMRALVNKAFTPKAMKAWEPKIARITNELLQEVEHLEDIDIVEHLSYPLPVMVIADILGVPIEDQRQFKDWSDIIVLEKLQQEKMKANDELETYFYRIIEEKRTRPGDDIISVLLQAKEEGKQLTDEEIVGFSILLLIAGNETTTNLISNTIYCLMEDKASFERLKREKELLPSGIEEVLRYRSPVQALHRIVKEDVTLAGKKLKAGEHVVPWMGSAHRDAEYFEDPEVFKIDRKPNVHMAFGRGIHFCLGAPLARIEAKIMLAELIDRYPQMDWSPSFELKPIESTFVYGLKELLIRKNV 404
                                    32        42        52        62     || 84        94       104       114       124       134       144       154       164    || 184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404
                                                                        68|                                                                                     169|                                                                                                                                                                                                                                
                                                                         81                                                                                      180
   Legend:   → Mismatch (orange background)
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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 5L94)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L94)

(-) Gene Ontology  (7, 7)

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    Pro B:89 - Pro B:90   [ RasMol ]  
 
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  5l94
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 Related Entries

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

UniProtKB/TrEMBL
        D5DKI8_BACMD | D5DKI8: 5l90 5l91 5l92

(-) Related Entries Specified in the PDB File

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