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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TOLUENE/O-XYLENE MONOOXYGENASE HYDROXUYLASE FROM PSEUDOMONAS STUTZERI-AZIDE BOUND
 
Authors :  M. H. Sazinsky, J. Bard, A. Di Donato, S. J. Lippard
Date :  12 Apr 04  (Deposition) - 27 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Diiron, 4-Helix Bundle, Azide, Carboxylate Bridge, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. H. Sazinsky, J. Bard, A. Di Donato, S. J. Lippard
Crystal Structure Of The Toluene/O-Xylene Monooxygenase Hydroxylase From Pseudomonas Stutzeri Ox1: Insight Into The Substrate Specificity, Substrate Channeling, And Active Site Tuning Of Multicomponent Monooxygenases.
J. Biol. Chem. V. 279 30600 2004
PubMed-ID: 15096510  |  Reference-DOI: 10.1074/JBC.M400710200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TOLUENE, O-XYLENE MONOOXYGENASE OXYGENASE SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22BEA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET22A
    Gene: TOUA
    Organism Scientific: PSEUDOMONAS STUTZERI
    Organism Taxid: 316
    Other Details: ALPHA SUBUNIT
 
Molecule 2 - TOLUENE, O-XYLENE MONOOXYGENASE OXYGENASE SUBUNIT
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22BEA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET22
    Gene: TOUE
    Organism Scientific: PSEUDOMONAS STUTZERI
    Organism Taxid: 316
    Other Details: BETA SUBUNIT
 
Molecule 3 - TOUB
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22BEA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET22
    Gene: TOUB
    Organism Scientific: PSEUDOMONAS STUTZERI
    Organism Taxid: 316
    Other Details: GAMMA SUBUNIT

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1AZI1Ligand/IonAZIDE ION
2FE2Ligand/IonFE (III) ION
3OH1Ligand/IonHYDROXIDE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AZI2Ligand/IonAZIDE ION
2FE-1Ligand/IonFE (III) ION
3OH-1Ligand/IonHYDROXIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:134 , GLU A:197 , GLU A:231 , HIS A:234 , FE A:500 , OH A:501 , AZI A:502BINDING SITE FOR RESIDUE FE A 499
2AC2SOFTWAREGLU A:104 , GLU A:134 , HIS A:137 , FE A:499 , OH A:501 , AZI A:502 , HOH A:503BINDING SITE FOR RESIDUE FE A 500
3AC3SOFTWAREGLU A:134 , HIS A:137 , GLU A:231 , HIS A:234 , FE A:499 , FE A:500 , AZI A:502 , HOH A:503BINDING SITE FOR RESIDUE OH A 501
4AC4SOFTWAREGLU A:104 , GLU A:134 , PHE A:196 , GLU A:197 , FE A:499 , FE A:500 , OH A:501 , HOH A:503 , HOH A:580BINDING SITE FOR RESIDUE AZI A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T0R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:460 -Pro A:461

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T0R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T0R)

(-) Exons   (0, 0)

(no "Exon" information available for 1T0R)

(-) 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:491
 aligned with O87798_PSEST | O87798 from UniProtKB/TrEMBL  Length:498

    Alignment length:491
                                    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       391       401       411       421       431       441       451       461       471       481       491 
         O87798_PSEST     2 SMLKREDWYDLTRTTNWTPKYVTENELFPEEMSGARGISMEAWEKYDEPYKITYPEYVSIQREKDSGAYSIKAALERDGFVDRADPGWVSTMQLHFGAIALEEYAASTAEARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDMMMTRDSVAVSIMLTFAFETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLFSVLTGPIMDYYTPLESRNQSFKEFMLEWIVAQFERQLLDLGLDKPWYWDQFMQDLDETHHGMHLGVWYWRPTVWWDPAAGVSPEEREWLEEKYPGWNDTWGQCWDVITDNLVNGKPELTVPETLPTICNMCNLPIAHTPGNKWNVKDYQLEYEGRLYHFGSEADRWCFQIDPERYKNHTNLVDRFLKGEIQPADLAGALMYMSLEPGVMGDDAHDYEWVKAYQ 492
               SCOP domains d1t0ra_ A: Toluene, o-xylene monooxygenase oxygenase subunit TouA                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------Phenol_Hydrox-1t0rA01 A:17-251                                                                                                                                                                                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------YHS-1t0rA02 A:405-448                       -------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.........hhhhhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh..................hhhhh......eee..eee...hhhhhhhhhhhhhhh....hhhhhhhh......hhhhhhhhh.............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0r A   2 SMLKREDWYDLTRTTNWTPKYVTENELFPEEMSGARGISMEAWEKYDEPYKITYPEYVSIQREKDSGAYSIKAALERDGFVDRADPGWVSTMQLHFGAIALEEYAASTAEARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDMMMTRDSVAVSIMLTFAFETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLFSVLTGPIMDYYTPLESRNQSFKEFMLEWIVAQFERQLLDLGLDKPWYWDQFMQDLDETHHGMHLGVWYWRPTVWWDPAAGVSPEEREWLEEKYPGWNDTWGQCWDVITDNLVNGKPELTVPETLPTICNMCNLPIAHTPGNKWNVKDYQLEYEGRLYHFGSEADRWCFQIDPERYKNHTNLVDRFLKGEIQPADLAGALMYMSLEPGVMGDDAHDYEWVKAYQ 492
                                    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       391       401       411       421       431       441       451       461       471       481       491 


Chain B from PDB  Type:PROTEIN  Length:323
 aligned with O87802_PSEST | O87802 from UniProtKB/TrEMBL  Length:330

    Alignment length:323
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327   
         O87802_PSEST     8 ALKPLKTWSHLAGNRRRPSEYEVVSTNLHYFTDNPERPWELDSNLPMQTWYKKYCFDSPLKHDDWNAFRDPDQLVYRTYNLLQDGQESYVQGLFDQLNDRGHDQMLTREWVETLARFYTPARYLFHALQMGSVYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELANCYPDVGFGKRERDVWENDPAWQGFRELIEKALIAWDWGEAFTAINLVTKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGNREVLQKWVAKWEPLADKAIEAYCSALPDGENAIVEAKSASRYVRQMMGL 330
               SCOP domains d1t0rb_ B: Toluene, o-xylene monooxygenase oxygenase subunit TouE                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1t0rB00 B:8-330 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------Phenol_Hydrox-1t0rB01 B:56-281                                                                                                                                                                                                    ------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhh...hhhhh..........hhhhhhhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0r B   8 ALKPLKTWSHLAGNRRRPSEYEVVSTNLHYFTDNPERPWELDSNLPMQTWYKKYCFDSPLKHDDWNAFRDPDQLVYRTYNLLQDGQESYVQGLFDQLNDRGHDQMLTREWVETLARFYTPARYLFHALQMGSVYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELANCYPDVGFGKRERDVWENDPAWQGFRELIEKALIAWDWGEAFTAINLVTKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGNREVLQKWVAKWEPLADKAIEAYCSALPDGENAIVEAKSASRYVRQMMGL 330
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327   


Chain C from PDB  Type:PROTEIN  Length:84
 aligned with O87799_PSEST | O87799 from UniProtKB/TrEMBL  Length:86

    Alignment length:84
                                    11        21        31        41        51        61        71        81    
         O87799_PSEST     2 ATFPIMSNFERDFVIQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFMD  85
               SCOP domains d1t0rc_ C: Toluene, o-xylene monooxygenase oxygenase subunit TouB                    SCOP domains
               CATH domains 1t0rC00 C:2-85 TmoB-like (Pfam 06234). Chain C                                       CATH domains
               Pfam domains TmoB-1t0rC01 C:2-85                                                                  Pfam domains
         Sec.struct. author .eeeeeeee.....eeeeeee...hhhhhhhhhhh.............eeeeee.....ee....hhhhhh....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1t0r C   2 ATFPIMSNFERDFVIQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFMD  85
                                    11        21        31        41        51        61        71        81
   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  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (3, 4)

Asymmetric Unit
(-)
Clan: Ferritin (185)
(-)
Clan: TRASH (61)
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (6, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (O87798_PSEST | O87798)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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.

Chain B   (O87802_PSEST | O87802)
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:0016709    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
biological process
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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.

Chain C   (O87799_PSEST | O87799)
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.
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.

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  1t0r
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  O87798_PSEST | O87798
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  O87799_PSEST | O87799
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  O87802_PSEST | O87802
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 Related Entries

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

UniProtKB/TrEMBL
        O87798_PSEST | O87798: 1t0q 1t0s 2inc 2ind 2rdb
        O87799_PSEST | O87799: 1t0q 1t0s 2inc 2ind 2rdb
        O87802_PSEST | O87802: 1t0q 1t0s 2inc 2ind 2rdb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1T0R)