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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHAN 2,3-DIOXYGENASE (TDO) FROM XANTHOMONAS CAMPESTRIS IN COMPLEX WITH FERRIC HEME. NORTHEAST STRUCTURAL GENOMICS TARGET XCR13
 
Authors :  F. Forouhar, J. L. R. Anderson, C. G. Mowat, A. Hussain, C. Bruckmann, S. J. Thackray, J. Seetharaman, T. Tucker, C. K. Ho, L. C. Ma, K. Cunningham, H. Janjua, L. Zhao, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, S. K. Chapman, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  14 Nov 06  (Deposition) - 19 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPTOPHAN 2,3-DIOXYGENASE
    Atcc: 33913
    Chains: A, B, C, D
    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: XCC0432
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 340
    Strain: PV. CAMPESTRIS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:51 , HIS A:55 , TRP A:102 , LEU A:105 , SER A:124 , GLY A:125 , TYR A:131 , ARG A:132 , TRP A:236 , HIS A:240 , VAL A:244 , PHE A:262BINDING SITE FOR RESIDUE HEM A 401
2AC2SOFTWAREPHE B:51 , HIS B:55 , TRP B:102 , LEU B:105 , SER B:124 , GLY B:125 , PHE B:126 , TYR B:131 , HIS B:240 , VAL B:244 , GLY B:259 , PHE B:262 , LEU B:263 , TYR C:24BINDING SITE FOR RESIDUE HEM B 401
3AC3SOFTWAREPHE C:51 , HIS C:55 , LEU C:105 , SER C:124 , GLY C:125 , PHE C:126 , TYR C:131 , ARG C:132 , HIS C:240 , VAL C:244 , ILE C:248 , PHE C:262BINDING SITE FOR RESIDUE HEM C 401
4AC4SOFTWAREPHE D:51 , HIS D:55 , LEU D:105 , SER D:124 , GLY D:125 , PHE D:126 , TYR D:131 , HIS D:240 , VAL D:244 , PHE D:262 , LEU D:263BINDING SITE FOR RESIDUE HEM D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NW7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NW7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NW7)

(-) Exons   (0, 0)

(no "Exon" information available for 2NW7)

(-) 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:259
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:264
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           T23O_XANCP    21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV 284
               SCOP domains d2nw7a_ A: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----..hhhhhhhhh....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nw7 A  21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFK-----SSGVGFLQQALALTFFPELFDVRTSVGV 284
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250|     |260       270       280    
                                                                                                                                                                                                                                                                251   257                           


Chain B from PDB  Type:PROTEIN  Length:259
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:264
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           T23O_XANCP    21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV 284
               SCOP domains d2nw7b_ B: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhh.........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----..hhhhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nw7 B  21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFK-----SSGVGFLQQALALTFFPELFDVRTSVGV 284
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250|     |260       270       280    
                                                                                                                                                                                                                                                                251   257                           


Chain C from PDB  Type:PROTEIN  Length:259
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:264
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           T23O_XANCP    21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV 284
               SCOP domains d2nw7c_ C: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhh..........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-----..hhhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nw7 C  21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFK-----SSGVGFLQQALALTFFPELFDVRTSVGV 284
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250|     |260       270       280    
                                                                                                                                                                                                                                                                251   257                           


Chain D from PDB  Type:PROTEIN  Length:260
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:264
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           T23O_XANCP    21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV 284
               SCOP domains d2nw7d_ D: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw7D01 D:196-282                                                      -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw7D02 D:196-282                                                      -- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw7D03 D:196-282                                                      -- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw7D04 D:196-282                                                      -- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw7D05 D:196-282                                                      -- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw7D06 D:196-282                                                      -- Pfam domains (6)
           Pfam domains (7) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw7D07 D:196-282                                                      -- Pfam domains (7)
           Pfam domains (8) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw7D08 D:196-282                                                      -- Pfam domains (8)
         Sec.struct. author ..hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....----.....hhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nw7 D  21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKR----SSGVGFLQQALALTFFPELFDVRTSVGV 284
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 |    |260       270       280    
                                                                                                                                                                                                                                                                 252  257
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NW7)

(-) Pfam Domains  (1, 8)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (T23O_XANCP | Q8PDA8)
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:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006569    tryptophan catabolic process    The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
    GO:0019442    tryptophan catabolic process to acetyl-CoA    The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including acetyl-CoA.
    GO:0019441    tryptophan catabolic process to kynurenine    The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including kynurenine.

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  2nw7
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 Related Entries

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

UniProtKB/Swiss-Prot
        T23O_XANCP | Q8PDA8: 1yw0 2nw8 2nw9 3bk9 3e08

(-) Related Entries Specified in the PDB File

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