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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE 2,3-DIOXYGENASE (SO4414) FROM SHEWANELLA ONEIDENSIS IN COMPLEX WITH FERRIC HEME. NORTHEAST STRUCTURAL GENOMICS TARGET SOR52.
 
Authors :  F. Forouhar, J. L. R. Anderson, C. G. Mowat, A. Hussain, J. Seetharaman, C. Bruckmann, S. J. Thackray, N. Khan, K. Cunningham, H. Janjua, L. Zha L. C. Ma, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, S. K. L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  14 Nov 06  (Deposition) - 19 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Dioxygenase, Heme-Binding Protein, Hemoprotein, All Alpha-Helical Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, J. L. Anderson, C. G. Mowat, S. M. Vorobiev, A. Hussain, M. Abashidze, C. Bruckmann, S. J. Thackray, J. Seetharaman, T. Tucker R. Xiao, L. C. Ma, L. Zhao, T. B. Acton, G. T. Montelione, S. K. Chapman, L. Tong
Molecular Insights Into Substrate Recognition And Catalysis By Tryptophan 2, 3-Dioxygenase.
Proc. Natl. Acad. Sci. Usa V. 104 473 2007
PubMed-ID: 17197414  |  Reference-DOI: 10.1073/PNAS.0610007104

(-) Compounds

Molecule 1 - CONSERVED DOMAIN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector: PET21
    Expression System Vector Type: PLASMID
    Gene: SO_4414
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1
    Synonym: PUTATIVE 2,3-DIOXYGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:152 , ASN A:156 , ASN A:201 , LEU A:204 , ASN A:235 , ALA A:236 , GLY A:237 , ILE A:242 , HIS A:324 , TYR A:332 , ILE A:333 , LEU A:365 , ARG A:369 , HOH A:404 , HOH A:493BINDING SITE FOR RESIDUE HEM A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NWB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NWB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NWB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NWB)

(-) Exons   (0, 0)

(no "Exon" information available for 2NWB)

(-) 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:379
 aligned with Q8E972_SHEON | Q8E972 from UniProtKB/TrEMBL  Length:392

    Alignment length:392
                                                                                                                                                                                                                                                                                                                                                                                                                             392    
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       | -  
         Q8E972_SHEON     5 TYNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYMAACRRHEITEPTRETTSPLLEASALAMHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQMLVDKFLYMMPEDQQILRECMRRPNLMDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKYIAEPSVSMEQQHLAKVTASGPPLHVLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLR----   -
               SCOP domains d2nwba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhh.....hhhhhh....ee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee..eee.......hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nwb A   5 TYNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYMAACRRHEITEPTRETTSPLLEASALAMHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQMLVDKFLYMMPEDQQILRECMRRPNLMDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKYIAEPSVSM-------------PLHVLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLRLEHH 396
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334     |   -       354       364       374       384       394  
                                                                                                                                                                                                                                                                                                                                                                         340           354                                          


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with Q8E972_SHEON | Q8E972 from UniProtKB/TrEMBL  Length:392

    Alignment length:389
                                                                                                                                                                                                                                                                                                                                                                                                                            392  
                                    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      |  
         Q8E972_SHEON     6 YNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYMAACRRHEITEPTRETTSPLLEASALAMHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQMLVDKFLYMMPEDQQILRECMRRPNLMDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKYIAEPSVSMEQQHLAKVTASGPPLHVLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLR--   -
               SCOP domains d2nwbb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DUF1864-2nwbB01 B:6-391                                                                                                                                                                                                                                                                                                                                                                           --- Pfam domains (1)
           Pfam domains (2) DUF1864-2nwbB02 B:6-391                                                                                                                                                                                                                                                                                                                                                                           --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhh.....hhhhhh....ee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee..eee.......hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......------------------------.hhhhhhhhhhhhhh........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nwb B   6 YNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYMAACRRHEITEPTRETTSPLLEASALAMHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQMLVDKFLYMMPEDQQILRECMRRPNLMDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKY------------------------VLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLRLE 394
                                    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      |  -         -         - |     365       375       385         
                                                                                                                                                                                                                                                                                                                                                                332                      357
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NWB)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: IDO-like (6)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8E972_SHEON | Q8E972)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0004833    tryptophan 2,3-dioxygenase activity    Catalysis of the reaction: L-tryptophan + O2 = N-formyl-L-kynurenine.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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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  2nwb
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 Related Entries

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

UniProtKB/TrEMBL
        Q8E972_SHEON | Q8E972: 1zee

(-) Related Entries Specified in the PDB File

1yw0 STRUCTURAL HOMOLOG IN APO FORM
1zee THE SAME PROTEIN IN APO FORM
2nw7 STRUCTURAL HOMOLOG IN COMPLEX WITH FERRIC HEME
2nw8 STRUCTURAL HOMOLOG IN COMPLEX WITH FERROUS HEME AND TRYPTOPHAN
2nw9 STRUCTURAL HOMOLOG IN COMPLEX WITH FERROUS HEME AND 6- FLUORO-L-TRYPTOPHAN