Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  PHENYLACETONE MONOOXYGENASE: REDUCED ENZYME IN COMPLEX WITH APADP
 
Authors :  C. Martinoli, M. W. Fraaije, A. Mattevi
Date :  19 Sep 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Flavin, Baeyer-Villiger, Cofactor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Martinoli, H. M. Dudek, R. Orru, D. E. Edmondson, M. W. Fraaije, A. Mattevi
Beyond The Protein Matrix: Probing Cofactor Variants In A Baeyer-Villiger Oxygenation Reaction.
Acs Catal. V. 3 3058 2013
PubMed-ID: 24443704  |  Reference-DOI: 10.1021/CS400837Z

(-) Compounds

Molecule 1 - PHENYLACETONE MONOOXYGENASE
    Chains: A
    EC Number: 1.14.13.92
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PBAD
    Expression System Taxid: 83333
    Expression System Variant: TOP10
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOBIFIDA FUSCA
    Organism Taxid: 2021
    Synonym: PAMO, BAEYER-VILLIGER MONOOXYGENASE, BVMO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2N011Ligand/Ion3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE
3P6G1Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:22 , GLY A:23 , GLY A:25 , PHE A:26 , SER A:27 , GLU A:46 , THR A:47 , GLY A:53 , VAL A:54 , TRP A:55 , TRP A:57 , ASN A:58 , CYS A:65 , ASP A:66 , ILE A:67 , TYR A:72 , THR A:117 , THR A:118 , VAL A:119 , ALA A:149 , SER A:150 , GLY A:151 , GLN A:152 , ILE A:399 , MET A:446 , ILE A:450 , N01 A:701 , HOH A:2005 , HOH A:2006 , HOH A:2013 , HOH A:2063 , HOH A:2068 , HOH A:2167BINDING SITE FOR RESIDUE FAD A 700
2AC2SOFTWARETYR A:60 , ARG A:64 , CYS A:65 , ASP A:66 , LEU A:153 , PRO A:159 , ASN A:160 , PHE A:161 , GLY A:193 , THR A:194 , GLY A:195 , SER A:196 , SER A:197 , GLN A:200 , ARG A:217 , THR A:218 , HIS A:220 , LYS A:336 , ARG A:337 , ALA A:386 , THR A:387 , GLY A:388 , PHE A:389 , TRP A:501 , FAD A:700 , HOH A:2075 , HOH A:2076 , HOH A:2081 , HOH A:2088 , HOH A:2090 , HOH A:2091 , HOH A:2092 , HOH A:2144 , HOH A:2165 , HOH A:2203 , HOH A:2204 , HOH A:2206 , HOH A:2217BINDING SITE FOR RESIDUE N01 A 701
3AC3SOFTWAREGLU A:272 , ARG A:279 , TYR A:280 , GLU A:283 , HOH A:2119 , HOH A:2218BINDING SITE FOR RESIDUE P6G A1543

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C74)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C74)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C74)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C74)

(-) Exons   (0, 0)

(no "Exon" information available for 4C74)

(-) 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:531
 aligned with PAMO_THEFY | Q47PU3 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:531
                                    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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541 
           PAMO_THEFY    12 QPPEEVDVLVVGAGFSGLYALYRLRELGRSVHVIETAGDVGGVWYWNRYPGARCDIESIEYCYSFSEEVLQEWNWTERYASQPEILRYINFVADKFDLRSGITFHTTVTAAAFDEATNTWTVDTNHGDRIRARYLIMASGQLSVPQLPNFPGLKDFAGNLYHTGNWPHEPVDFSGQRVGVIGTGSSGIQVSPQIAKQAAELFVFQRTPHFAVPARNAPLDPEFLADLKKRYAEFREESRNTPGGTHRYQGPKSALEVSDEELVETLERYWQEGGPDILAAYRDILRDRDANERVAEFIRNKIRNTVRDPEVAERLVPKGYPFGTKRLILEIDYYEMFNRDNVHLVDTLSAPIETITPRGVRTSEREYELDSLVLATGFDALTGALFKIDIRGVGNVALKEKWAAGPRTYLGLSTAGFPNLFFIAGPGSPSALSNMLVSIEQHVEWVTDHIAYMFKNGLTRSEAVLEKEDEWVEHVNEIADETLYPMTASWYTGANVPGKPRVFMLYVGGFHRYRQICDEVAAKGYEGFVLT 542
               SCOP domains d4c74a1 A:12-154,A:390-542 Phenylacetone monooxygenase                                                                                         d4c74a2 A:155-389 Phenylacetone monooxygenase                                                                                                                                                                                              d4c74a1 A:12-154,A:390-542 Phenylacetone monooxygenase                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhhh...eeee.......hhhhhh..................hhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.ee....eeeeeee....eeeeee....eeeeeeeee..............hhhhh..eeee.hhh..........eeeee..hhhhhhhhhhhhh...eeeeee.....eee......hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhh...........eee.hhhhhh....eeeee.....eeee...eeee...eee..eeee.......hhhhhh.eeehhhhhhhhhhh.................eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh.hhhhh.hhhhh...............hhhhhhhhhhhhhhh....eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c74 A  12 QPPEEVDVLVVGAGFSGLYALYRLRELGRSVHVIETAGDVGGVWYWNRYPGARCDIESIEYCYSFSEEVLQEWNWTERYASQPEILRYINFVADKFDLRSGITFHTTVTAAAFDEATNTWTVDTNHGDRIRARYLIMASGQLSVPQLPNFPGLKDFAGNLYHTGNWPHEPVDFSGQRVGVIGTGSSGIQVSPQIAKQAAELFVFQRTPHFAVPARNAPLDPEFLADLKKRYAEFREESRNTPGGTHRYQGPKSALEVSDEELVETLERYWQEGGPDILAAYRDILRDRDANERVAEFIRNKIRNTVRDPEVAERLVPKGYPFGTKRLILEIDYYEMFNRDNVHLVDTLSAPIETITPRGVRTSEREYELDSLVLATGFDALTGALFKIDIRGVGNVALKEKWAAGPRTYLGLSTAGFPNLFFIAGPGSPSALSNMLVSIEQHVEWVTDHIAYMFKNGLTRSEAVLEKEDEWVEHVNEIADETLYPMTASWYTGANVPGKPRVFMLYVGGFHRYRQICDEVAAKGYEGFVLT 542
                                    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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C74)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C74)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAMO_THEFY | Q47PU3)
molecular function
    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.
    GO:0033776    phenylacetone monooxygenase activity    Catalysis of the reaction: H(+) + NADPH + O(2) + phenylacetone = benzyl acetate + H(2)O + NADP(+).
biological process
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    N01  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P6G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4c74)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4c74
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PAMO_THEFY | Q47PU3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.13.92
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PAMO_THEFY | Q47PU3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PAMO_THEFY | Q47PU3: 1w4x 2ylr 2yls 2ylt 2ylw 2ylx 2ylz 2ym1 2ym2 4c77 4d03 4d04 4ovi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4C74)