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(-) Description

Title :  THE 2.1 A CRYSTAL STRUCTURE OF CYP109E1 FROM BACILLUS MEGATERIUM IN COMPLEX WITH CORTICOSTERONE
 
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 :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bacillus, Bacterial Proteins, Binding Sites, Catalysis, Corticosterone, 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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1C0R1Ligand/IonCORTICOSTERONE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MLA1Ligand/IonMALONIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1C0R1Ligand/IonCORTICOSTERONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MLA1Ligand/IonMALONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1C0R-1Ligand/IonCORTICOSTERONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MLA-1Ligand/IonMALONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:84 , ILE A:85 , HIS A:92 , ARG A:96 , LEU A:238 , LEU A:239 , ALA A:242 , THR A:246 , THR A:247 , LEU A:250 , LEU A:292 , ARG A:294 , ALA A:344 , PHE A:345 , GLY A:346 , ILE A:349 , HIS A:350 , CYS A:352 , GLY A:354 , ALA A:358 , C0R A:502 , MLA A:503 , HOH A:613 , HOH A:629binding site for residue HEM A 501
2AC2SOFTWAREILE A:168 , LEU A:238 , ILE A:241 , ALA A:242 , PHE A:391 , HEM A:501 , MLA A:503binding site for residue C0R A 502
3AC3SOFTWAREARG A:69 , ILE A:85 , LEU A:292 , HIS A:293 , ARG A:294 , PHE A:391 , HEM A:501 , C0R A:502binding site for residue MLA A 503
4AC4SOFTWARELEU 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 , LEU B:357 , ALA B:358 , HOH B:617 , HOH B:619 , HOH B:624 , HOH B:632binding site for residue HEM B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L92)

(-) 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 5L92)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L92)

(-) Exons   (0, 0)

(no "Exon" information available for 5L92)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhhh...eeee....eeee.hhhhhhhhhhh...ee.........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....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
                 5l92 A  16 IQTKEERFNPFSWYEEMRNTAPVQWDEERQVWDVFHYDGVKEVLEQKNIFSSDRRPQRQTALGTSLINIDPPKHAEMRALVNKAFTPKAMKAWEPKIARITNELLQEVEHLEDIDIVEHLSYPLPVMVIADILGVPIEDQRQFKDWSDIIVAGPSNNERETLEKLQQEKMKANDELETYFYRIIEEKRTRPGDDIISVLLQAKEEGKQLTDEEIVGFSILLLIAGNETTTNLISNTIYCLMEDKASFERLKREKELLPSGIEEVLRYRSPVQALHRIVKEDVTLAGKKLKAGEHVVPWMGSAHRDAEYFEDPEVFKIDRKPNVHMAFGRGIHFCLGAPLARIEAKIMLAELIDRYPQMDWSPSFELKPIESTFVYGLKELLIRKNV 404
                                    25        35        45        55        65     || 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      
                                                                                  71|                                                                                                                                                                                                                                                                                                                                         
                                                                                   75                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.eeee....eeee.hhhhhhhhhhh...eee...hhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee....................eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l92 B  19 KEERFNPFSWYEEMRNTAPVQWDEERQVWDVFHYDGVKEVLEQKNIFSSDGTSLINIDPPKHAEMRALVNKAFTPKAMKAWEPKIARITNELLQEVEHLEDIDIVEHLSYPLPVMVIADILGVPIEDQRQFKDWSDIIVNNERETLEKLQQEKMKANDELETYFYRIIEEKRTRPGDDIISVLLQAKEEGKQLTDEEIVGFSILLLIAGNETTTNLISNTIYCLMEDKASFERLKREKELLPSGIEEVLRYRSPVQALHRIVKEDVTLAGKKLKAGEHVVPWMGSAHRDAEYFEDPEVFKIDRKPNVHMAFGRGIHFCLGAPLARIEAKIMLAELIDRYPQMDWSPSFELKPIESTFVYGLKELLIRKNV 404
                                    28        38        48        58        68|       90       100       110       120       130       140       150       160       174       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                                                                                      174
   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  (0, 0)

(no "SCOP Domain" information available for 5L92)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L92)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L92)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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    Lys A:338 - Pro A:339   [ RasMol ]  
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  5l92
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 Related Entries

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        D5DKI8_BACMD | D5DKI8: 5l90 5l91 5l94

(-) Related Entries Specified in the PDB File

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