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(-) Description

Title :  CARBAZOLE- AND OXYGEN-BOUND OXYGENASE WITH ILE262 REPLACED BY VAL AND FERREDOXIN COMPLEX OF CARBAZOLE 1,9A-DIOXYGENASE
 
Authors :  Y. Ashikawa, Y. Usami, K. Inoue, H. Nojiri
Date :  23 Oct 13  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rieske Non-Heme Iron Oxygenase, Carbazole 1, 9A-Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Inoue, Y. Usami, Y. Ashikawa, H. Noguchi, T. Umeda, A. Yamagami-Ashikawa, T. Horisaki, H. Uchimura, T. Terada, S. Nakamura, K. Shimizu, H. Habe, H. Yamane, Z. Fujimoto, H. Nojiri
Structural Basis Of The Divergent Oxygenation Reactions Catalyzed By The Rieske Non-Heme Iron Oxygenase, Carbazole 1, 9A-Dioxygenase
Appl. Environ. Microbiol. 2014
PubMed-ID: 24584240  |  Reference-DOI: 10.1128/AEM.04000-13

(-) Compounds

Molecule 1 - TERMINAL OXYGENASE COMPONENT OF CARBAZOLE
    Chains: A, B, C
    EC Number: 1.14.12.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEI262V
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CARAA
    Mutation: YES
    Organism Scientific: JANTHINOBACTERIUM
    Organism Taxid: 213804
    Strain: J3
    Synonym: TERMINAL OXYGENASE COMPONENT OF CARBAZOLE 1,9A-DIOXYGENASE
 
Molecule 2 - FERREDOXIN CARAC
    Chains: D, E, F
    EC Number: 1.14.12.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PECAC1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CARAC
    Organism Scientific: PSEUDOMONAS RESINOVORANS
    Organism Taxid: 53412
    Strain: CA10
    Synonym: FERREDOXIN OF CARBAZOLE 1,9A-DIOXYGENASE, CARDO

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
19CA2Ligand/Ion9H-CARBAZOLE
2FE23Ligand/IonFE (II) ION
3FES6Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4OXY3Ligand/IonOXYGEN MOLECULE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:183 , HIS A:187 , ASP A:333 , OXY A:503BINDING SITE FOR RESIDUE FE2 A 501
02AC2SOFTWARECYS A:69 , HIS A:71 , ARG A:72 , VAL A:74 , CYS A:90 , HIS A:93 , TRP A:95BINDING SITE FOR RESIDUE FES A 502
03AC3SOFTWAREHIS A:183 , HIS A:187 , ASN A:330 , ASP A:333 , FE2 A:501 , HOH A:647BINDING SITE FOR RESIDUE OXY A 503
04AC4SOFTWAREHIS B:183 , HIS B:187 , ASP B:333 , OXY B:503BINDING SITE FOR RESIDUE FE2 B 501
05AC5SOFTWARECYS B:69 , HIS B:71 , ARG B:72 , CYS B:90 , TYR B:92 , HIS B:93 , ALA B:94 , TRP B:95BINDING SITE FOR RESIDUE FES B 502
06AC6SOFTWAREHIS B:183 , HIS B:187 , PHE B:329 , ASN B:330 , ASP B:333 , FE2 B:501 , 9CA B:504BINDING SITE FOR RESIDUE OXY B 503
07AC7SOFTWAREGLY B:178 , ALA B:259 , LEU B:270 , VAL B:272 , PHE B:275 , GLN B:282 , GLU B:284 , PHE B:329 , ASN B:330 , OXY B:503BINDING SITE FOR RESIDUE 9CA B 504
08AC8SOFTWAREHIS C:183 , HIS C:187 , ASP C:333 , OXY C:503BINDING SITE FOR RESIDUE FE2 C 501
09AC9SOFTWARECYS C:69 , HIS C:71 , ARG C:72 , CYS C:90 , TYR C:92 , HIS C:93 , ALA C:94 , TRP C:95BINDING SITE FOR RESIDUE FES C 502
10BC1SOFTWAREHIS C:183 , HIS C:187 , ASP C:333 , FE2 C:501 , 9CA C:504 , HOH C:626BINDING SITE FOR RESIDUE OXY C 503
11BC2SOFTWAREGLY C:178 , HIS C:183 , LEU C:270 , VAL C:272 , PHE C:275 , GLN C:282 , PHE C:329 , ASN C:330 , OXY C:503BINDING SITE FOR RESIDUE 9CA C 504
12BC3SOFTWARECYS D:46 , HIS D:48 , GLY D:49 , CYS D:65 , HIS D:68 , GLY D:70BINDING SITE FOR RESIDUE FES D 201
13BC4SOFTWARECYS E:46 , HIS E:48 , GLY E:49 , CYS E:65 , HIS E:68 , GLY E:70BINDING SITE FOR RESIDUE FES E 201
14BC5SOFTWARECYS F:46 , HIS F:48 , GLY F:49 , CYS F:65 , HIS F:68 , GLY F:70BINDING SITE FOR RESIDUE FES F 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NBB)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Leu A:266 -Pro A:267
2Asn A:273 -Pro A:274
3Phe A:275 -Pro A:276
4Leu B:266 -Pro B:267
5Asn B:273 -Pro B:274
6Phe B:275 -Pro B:276
7Leu C:266 -Pro C:267
8Asn C:273 -Pro C:274
9Phe C:275 -Pro C:276
10Ser D:82 -Pro D:83
11Ser E:82 -Pro E:83
12Ser F:82 -Pro F:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NBB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NBB)

(-) Exons   (0, 0)

(no "Exon" information available for 4NBB)

(-) 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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..hhhhhhh......eeeeeee.hhh.....eeeee..eeeeeeee..eeeeee........hhhhhh......eee.....eeee.....eeee...............ee.eeee..eeeeee......hhhhhh........eeeeee..ee..hhhhhhhhhhhhhhhhhhh.hhhhhhh..ee..eee...hhhh.eeee........eeeehhhhhheee.eeee..eeeee.ee.......eeeee...eeeee.......eeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbb A   2 ANVDEAILKRVKGWAPYVDAKLGFRNHWYPVMFSKEINEGEPKTLKLLGENLLVNRIDGKLYCLKDRCLHRGVQLSVKVECKTKSTITCWYHAWTYRWEDGVLCDILTNPTSAQIGRQKLKTYPVQEAKGCVFIYLGDGDPPPLARDTPPNFLDDDMEILGKNQIIKSNWRLAVENGFDPSHIYIHKDSILVKDNDLALPLGFAPGGDRKQQTRVVDDDVVGRKGVYDLIGEHGVPVFEGTIGGEVVREGAYGEKIVANDVSIWLPGVLKVNPFPNPDMMQFEWYVPIDENTHYYFQTLGKPCANDEERKKYEQEFESKWKPMALEGFNNDDIWAREAMVDFYADDKGWVNEILFESDEAIVAWRKLASEHNQGIQTQAHVSGLEHH 388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       


Chain B from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..hhhhhhh......eeeeeee.hhh.....eeeee..eeeeeeee..eeeeee........hhhhhh......eee.....eeee.....eeee...............ee.eeee..eeeeee......hhhhhh........eeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhh.eee..eee....hhh.eeee........eeeehhhhhheee.eeee..eeeee.ee..ee...eeeee...eeeee.......eeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbb B   2 ANVDEAILKRVKGWAPYVDAKLGFRNHWYPVMFSKEINEGEPKTLKLLGENLLVNRIDGKLYCLKDRCLHRGVQLSVKVECKTKSTITCWYHAWTYRWEDGVLCDILTNPTSAQIGRQKLKTYPVQEAKGCVFIYLGDGDPPPLARDTPPNFLDDDMEILGKNQIIKSNWRLAVENGFDPSHIYIHKDSILVKDNDLALPLGFAPGGDRKQQTRVVDDDVVGRKGVYDLIGEHGVPVFEGTIGGEVVREGAYGEKIVANDVSIWLPGVLKVNPFPNPDMMQFEWYVPIDENTHYYFQTLGKPCANDEERKKYEQEFESKWKPMALEGFNNDDIWAREAMVDFYADDKGWVNEILFESDEAIVAWRKLASEHNQGIQTQAHVSGLEHH 388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       


Chain C from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..hhhhhhh......eeeeeee.hhh.....eeeee..eeeeeeee..eeeeee........hhhhhh......eee.....eeee.....eeee..................eeee..eeeeee......hhhhhh........eeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhh.eee..eee....hhh.eeee........eeeehhhhhheee.eeee..eeeee.ee..ee...eeeee...eeeee.......eeeeeeee.....eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbb C   2 ANVDEAILKRVKGWAPYVDAKLGFRNHWYPVMFSKEINEGEPKTLKLLGENLLVNRIDGKLYCLKDRCLHRGVQLSVKVECKTKSTITCWYHAWTYRWEDGVLCDILTNPTSAQIGRQKLKTYPVQEAKGCVFIYLGDGDPPPLARDTPPNFLDDDMEILGKNQIIKSNWRLAVENGFDPSHIYIHKDSILVKDNDLALPLGFAPGGDRKQQTRVVDDDVVGRKGVYDLIGEHGVPVFEGTIGGEVVREGAYGEKIVANDVSIWLPGVLKVNPFPNPDMMQFEWYVPIDENTHYYFQTLGKPCANDEERKKYEQEFESKWKPMALEGFNNDDIWAREAMVDFYADDKGWVNEILFESDEAIVAWRKLASEHNQGIQTQAHVSGLEHHH 389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        


Chain D from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhh.....eeeee..eeeeeeeee..eeeeee........hhhhheee..eee......eee.....eee........eeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4nbb D   4 IWLKVCAASDMQPGTIRRVNRVGAAPLAVYRVGDQFYATEDTCTHGIASLSEGTLDGDVIECPFHGGAFNVCTGMPASSPCTVPLGVFEVEVKEGEVYVAGEKK 107
                                    13        23        33        43        53        63        73        83        93       103    


Chain E from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.hhh....eeeeee..eeeeeeeee..eeeeee........hhhhheee..eee......eee.....eee...........eee...eeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4nbb E   2 NQIWLKVCAASDMQPGTIRRVNRVGAAPLAVYRVGDQFYATEDTCTHGIASLSEGTLDGDVIECPFHGGAFNVCTGMPASSPCTVPLGVFEVEVKEGEVYVAGEKKLEHHHHHH 115
                                    11        21        31        41        51        61        71        81        91       101       111    


Chain F from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeeeee..eeeeeeeee..eeeeee........hhhhheee..eee......eee.....eee...........eeee..eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4nbb F   4 IWLKVCAASDMQPGTIRRVNRVGAAPLAVYRVGDQFYATEDTCTHGIASLSEGTLDGDVIECPFHGGAFNVCTGMPASSPCTVPLGVFEVEVKEGEVYVAGEKK 107
                                    13        23        33        43        53        63        73        83        93       103
   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 4NBB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NBB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NBB)

(-) Gene Ontology  (8, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CARAC_PSERE | Q8GI16: 1vck 2de5 2de6 2de7 3vmg 3vmh 3vmi 4nb8 4nb9 4nba 4nbc 4nbd 4nbe 4nbf 4nbg 4nbh
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        Q84II6_JANS3 | Q84II6: 1ww9 2de5 2de6 2de7 3vmg 3vmh 3vmi 4nb8 4nb9 4nba 4nbc 4nbd 4nbe 4nbf 4nbg 4nbh

(-) Related Entries Specified in the PDB File

4nb8 4nb9 4nba 4nbc 4nbd 4nbe 4nbf 4nbg 4nbh