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(-) Description

Title :  CRYSTAL STRUCTURE OF OTEMO COMPLEX WITH FAD AND NADP (FORM 3)
 
Authors :  R. Shi, A. Matte, M. Cygler, P. Lau
Date :  17 Nov 11  (Deposition) - 01 Feb 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Baeyer-Villiger Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Leisch, R. Shi, S. Grosse, K. Morley, H. Bergeron, M. Cygler, H. Iwaki, Y. Hasegawa, P. C. Lau
Cloning, Baeyer-Villiger Biooxidations, And Structures Of The Camphor Pathway 2-Oxo-{Delta}(3)-4, 5, 5-Trimethylcyclopentenylacetyl-Coenzym A Monooxygenase Of Pseudomonas Putida Atcc 17453.
Appl. Environ. Microbiol. V. 78 2200 2012
PubMed-ID: 22267661  |  Reference-DOI: 10.1128/AEM.07694-11

(-) Compounds

Molecule 1 - OTEMO
    Chains: A, B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSD80
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OTEMO
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Strain: ATCC 17453

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , GLY A:18 , VAL A:19 , THR A:20 , GLU A:39 , ALA A:40 , GLY A:46 , THR A:47 , TRP A:48 , TRP A:50 , ASN A:51 , LEU A:58 , ASP A:59 , THR A:60 , TYR A:65 , THR A:110 , ARG A:111 , VAL A:112 , ALA A:142 , GLY A:144 , ILE A:399 , CYS A:444 , ASN A:445 , VAL A:446 , HOH A:547 , NAP A:552 , HOH A:555BINDING SITE FOR RESIDUE FAD A 551
2AC2SOFTWARETYR A:53 , ARG A:57 , LEU A:58 , ASP A:59 , LEU A:146 , PRO A:152 , GLY A:192 , THR A:193 , GLY A:194 , ALA A:195 , THR A:196 , GLN A:199 , ARG A:216 , THR A:217 , LYS A:336 , ARG A:337 , ILE A:358 , ALA A:386 , THR A:387 , GLY A:388 , TRP A:501 , FAD A:551BINDING SITE FOR RESIDUE NAP A 552
3AC3SOFTWAREGLY B:16 , GLY B:18 , VAL B:19 , THR B:20 , GLU B:39 , ALA B:40 , GLY B:46 , THR B:47 , TRP B:50 , TYR B:53 , LEU B:58 , ASP B:59 , THR B:60 , TYR B:65 , THR B:110 , ARG B:111 , VAL B:112 , ALA B:142 , THR B:143 , GLY B:144 , PRO B:145 , SER B:147 , ILE B:399 , CYS B:444 , ASN B:445 , VAL B:446 , HOH B:550 , NAP B:552 , HOH B:573BINDING SITE FOR RESIDUE FAD B 551
4AC4SOFTWARETYR B:53 , ARG B:57 , LEU B:58 , ASP B:59 , ARG B:150 , PRO B:152 , ILE B:154 , GLY B:192 , THR B:193 , GLY B:194 , ALA B:195 , THR B:196 , GLN B:199 , ARG B:216 , THR B:217 , ARG B:337 , ILE B:358 , ALA B:386 , THR B:387 , GLY B:388 , TRP B:501 , HOH B:548 , FAD B:551 , HOH B:554 , HOH B:566 , HOH B:572BINDING SITE FOR RESIDUE NAP B 552

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:444 -A:449
2B:444 -B:449

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UP4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UP4)

(-) Exons   (0, 0)

(no "Exon" information available for 3UP4)

(-) 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:528
 aligned with OTEMO_PSEPU | H3JQW0 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:540
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545
          OTEMO_PSEPU     6 KSPALDAVVIGAGVTGIYQAFLINQAGMKVLGIEAGEDVGGTWYWNRYPGCRLDTESYAYGYFALKGIIPEWEWSENFASQPEMLRYVNRAADAMDVRKHYRFNTRVTAARYVENDRLWEVTLDNEEVVTCRFLISATGPLSASRMPDIKGIDSFKGESFHSSRWPTDAEGAPKGVDFTGKRVGVIGTGATGVQIIPIAAETAKELYVFQRTPNWCTPLGNSPMSKEKMDSLRNRYPTILEYVKSTDTAFPYHRDPRKGTDVSESERDAFFEELYRQPGYGIWLSGFRDLLLNKESNKFLADFVAKKIRQRVKDPVVAEKLIPKDHPFGAKRVPMETNYYETYNRDNVHLVDIREAPIQEVTPEGIKTADAAYDLDVIIYATGFDAVTGSLDRIDIRGKDNVRLIDAWAEGPSTYLGLQARGFPNFFTLVGPHNGSTFCNVGVCGGLQAEWVLRMISYMKDNGFTYSEPTQAAENRWTEEVYADFSRTLLAEANAWWVKTTTKPDGSVVRRTLVHVSGGPEYRKRCEQVAYNNYNGFELA 545
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhhhhhhh...eeee.......hhhhhh.........hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh.ee....eeeeeeehhhheeeeee...eeeeeeeeee..............hhhhh..eeee.hhh..---...........eeeee..hhhhhhhhhhhh....eeeeee......ee......hhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhh.............ee.hhhhhh....eeeee.....eeee...eeee...eee..eeee..............eeehhhhhhhhhhh.................eee...........hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhh....ee.---------.ee.....hhhhhhhhhhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3up4 A   6 KSPALDAVVIGAGVTGIYQAFLINQAGMKVLGIEAGEDVGGTWYWNRYPGCRLDTESYAYGYFALKGIIPEWEWSENFASQPEMLRYVNRAADAMDVRKHYRFNTRVTAARYVENDRLWEVTLDNEEVVTCRFLISATGPLSASRMPDIKGIDSFKGESFHSSRWPT---GAPKGVDFTGKRVGVIGTGATGVQIIPIAAETAKELYVFQRTPNWCTPLGNSPMSKEKMDSLRNRYPTILEYVKSTDTAFPYHRDPRKGTDVSESERDAFFEELYRQPGYGIWLSGFRDLLLNKESNKFLADFVAKKIRQRVKDPVVAEKLIPKDHPFGAKRVPMETNYYETYNRDNVHLVDIREAPIQEVTPEGIKTADAAYDLDVIIYATGFDAVTGSLDRIDIRGKDNVRLIDAWAEGPSTYLGLQARGFPNFFTLVGPHNGSTFCNVGVCGGLQAEWVLRMISYMKDNGFTYSEPTQAAENRWTEEVYADFSRTLLAEANAWWVKT---------RRTLVHVSGGPEYRKRCEQVAYNNYNGFELA 545
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165      |  -|      185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545
                                                                                                                                                                                                172 176                                                                                                                                                                                                                                                                                                                                      505       515                              


Chain B from PDB  Type:PROTEIN  Length:533
 aligned with OTEMO_PSEPU | H3JQW0 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:540
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545
          OTEMO_PSEPU     6 KSPALDAVVIGAGVTGIYQAFLINQAGMKVLGIEAGEDVGGTWYWNRYPGCRLDTESYAYGYFALKGIIPEWEWSENFASQPEMLRYVNRAADAMDVRKHYRFNTRVTAARYVENDRLWEVTLDNEEVVTCRFLISATGPLSASRMPDIKGIDSFKGESFHSSRWPTDAEGAPKGVDFTGKRVGVIGTGATGVQIIPIAAETAKELYVFQRTPNWCTPLGNSPMSKEKMDSLRNRYPTILEYVKSTDTAFPYHRDPRKGTDVSESERDAFFEELYRQPGYGIWLSGFRDLLLNKESNKFLADFVAKKIRQRVKDPVVAEKLIPKDHPFGAKRVPMETNYYETYNRDNVHLVDIREAPIQEVTPEGIKTADAAYDLDVIIYATGFDAVTGSLDRIDIRGKDNVRLIDAWAEGPSTYLGLQARGFPNFFTLVGPHNGSTFCNVGVCGGLQAEWVLRMISYMKDNGFTYSEPTQAAENRWTEEVYADFSRTLLAEANAWWVKTTTKPDGSVVRRTLVHVSGGPEYRKRCEQVAYNNYNGFELA 545
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhhhhhhh...eeee.......hhhhhh.........hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh.ee....eeeeeee....eeeeee...eeeeeeeeee..............hhhhh..eeee....................eeeee..hhhhhhhhhhhhh...eeeeee......ee......hhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhh.............ee..hhhhhhh..eeeee.....eeee...eeee...eee..eeee.......hhhhhh.eeehhhhhhhhhhh.................eee...........hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhh....ee.-------...ee.....hhhhhhhhhhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3up4 B   6 KSPALDAVVIGAGVTGIYQAFLINQAGMKVLGIEAGEDVGGTWYWNRYPGCRLDTESYAYGYFALKGIIPEWEWSENFASQPEMLRYVNRAADAMDVRKHYRFNTRVTAARYVENDRLWEVTLDNEEVVTCRFLISATGPLSASRMPDIKGIDSFKGESFHSSRWPTDAEGAPKGVDFTGKRVGVIGTGATGVQIIPIAAETAKELYVFQRTPNWCTPLGNSPMSKEKMDSLRNRYPTILEYVKSTDTAFPYHRDPRKGTDVSESERDAFFEELYRQPGYGIWLSGFRDLLLNKESNKFLADFVAKKIRQRVKDPVVAEKLIPKDHPFGAKRVPMETNYYETYNRDNVHLVDIREAPIQEVTPEGIKTADAAYDLDVIIYATGFDAVTGSLDRIDIRGKDNVRLIDAWAEGPSTYLGLQARGFPNFFTLVGPHNGSTFCNVGVCGGLQAEWVLRMISYMKDNGFTYSEPTQAAENRWTEEVYADFSRTLLAEANAWWVKT-------VVRRTLVHVSGGPEYRKRCEQVAYNNYNGFELA 545
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             505     513
   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 3UP4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UP4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UP4)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (OTEMO_PSEPU | H3JQW0)
molecular function
    GO:0004499    N,N-dimethylaniline monooxygenase activity    Catalysis of the reaction: N,N-dimethylaniline + NADPH + H+ + O2 = N,N-dimethylaniline N-oxide + NADP+ + H2O.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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.
biological process
    GO:0019383    (+)-camphor catabolic process    The chemical reactions and pathways resulting in the breakdown of (+)-camphor, a bicyclic monoterpene ketone.
    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/Swiss-Prot
        OTEMO_PSEPU | H3JQW0: 3uov 3uox 3uoy 3uoz 3up5

(-) Related Entries Specified in the PDB File

3uov OTEMO (FAD BOUND FORM 1)
3uox OTEMO (FAD BOUND FORM 2)
3uoy OTEMO COMPLEX WITH FAD AND NADP (FORM 1)
3uoz OTEMO COMPLEX WITH FAD AND NADP (FORM 2)
3up5 OTEMO COMPLEX WITH FAD AND NADP (FORM 4)