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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRYPTOPHAN 2,3-DIOXYGENASE FROM XANTHOMONAS CAMPESTRIS. NORTHEAST STRUCTURAL GENOMICS TARGET XCR13.
 
Authors :  S. M. Vorobiev, M. Abashidze, F. Forouhar, A. Kuzin, R. Xiao, M. Ciano, T. B. Aton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  16 Feb 05  (Deposition) - 15 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tryptophan, Dioxygenase, Nesg, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Vorobiev, M. Abashidze, F. Forouhar, A. Kuzin, R. Xiao, M. Ciano, T. B. Aton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Tryptophan 2, 3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target Xcr13.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPTOPHAN 2,3-DIOXYGENASE
    Chains: A, B, C, D
    EC Number: 1.13.11.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS STR. ATCC 33913
    Organism Taxid: 190485
    Strain: PV. CAMPESTRIS STR. ATCC 33913

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric/Biological Unit (2, 28)
No.NameCountTypeFull Name
1MG8Ligand/IonMAGNESIUM ION
2MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:27 , LEU B:28 , ALA C:36 , GLN C:37 , GLN C:38BINDING SITE FOR RESIDUE MG C 400
2AC2SOFTWAREALA A:36 , GLN A:37 , GLN A:38 , TYR D:27BINDING SITE FOR RESIDUE MG A 401
3AC3SOFTWARETYR A:27 , GLN D:38BINDING SITE FOR RESIDUE MG D 402
4AC4SOFTWAREALA B:36 , GLN B:37 , GLN B:38 , TYR C:27 , ARG C:29BINDING SITE FOR RESIDUE MG B 403
5AC5SOFTWARELEU B:108 , ARG B:246 , GLU D:224 , ARG D:279BINDING SITE FOR RESIDUE MG B 404
6AC6SOFTWAREGLN B:38 , LEU B:40 , TYR C:27BINDING SITE FOR RESIDUE MG B 405
7AC7SOFTWAREPHE A:126 , GLN A:127 , SER A:128BINDING SITE FOR RESIDUE MG A 406
8AC8SOFTWARELEU C:34 , SER C:35 , ALA C:36 , GLN C:37 , GLN C:38BINDING SITE FOR RESIDUE MG C 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YW0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu D:42 -Pro D:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YW0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YW0)

(-) Exons   (0, 0)

(no "Exon" information available for 1YW0)

(-) 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:243
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:262
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
           T23O_XANCP    23 TYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV 284
               SCOP domains d1yw0a1 A:23-284 Tryptophan 2,3-dioxygenase                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...----..hhhhhhhhhhh.....hhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yw0 A  23 TYGGYLRLDQLLSAQQPLSEPAHHDEmLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYmGFRDVLG----FQSLQYRYIEFLLGNKNPQmLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHmRTVmRVIGF---------------ALALTFFPELFDVRTSVGV 284
                                    32        42      | 52        62        72        82        92       102       112 |      |-   |   132       142  |    152       162       172       182       192       202       212       222       232       242  |    | -         -   |   272       282  
                                                     49-MSE                                                          114-MSE121  126                145-MSE                                                                                         241-MSE  250             266                  
                                                                                                                                                                                                                                                        245-MSE                                   


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:262
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
           T23O_XANCP    23 TYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV 284
               SCOP domains d1yw0b_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh......----..hhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhh............hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----------------.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yw0 B  23 TYGGYLRLDQLLSAQQPLSEPAHHDEmLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYmGFRDVLG----FQSLQYRYIEFLLGNKNPQmLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHmRTVmRVIGF----------------LALTFFPELFDVRTSVGV 284
                                    32        42      | 52        62        72        82        92       102       112 |      |-   |   132       142  |    152       162       172       182       192       202       212       222       232       242  |    | -         -    |  272       282  
                                                     49-MSE                                                          114-MSE121  126                145-MSE                                                                                         241-MSE  250              267                 
                                                                                                                                                                                                                                                        245-MSE                                   


Chain C from PDB  Type:PROTEIN  Length:243
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:262
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
           T23O_XANCP    23 TYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV 284
               SCOP domains d1yw0c_ C: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...----..hhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhh..........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yw0 C  23 TYGGYLRLDQLLSAQQPLSEPAHHDEmLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYmGFRDVLG----FQSLQYRYIEFLLGNKNPQmLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHmRTVmRVIGF---------------ALALTFFPELFDVRTSVGV 284
                                    32        42      | 52        62        72        82        92       102       112 |      |-   |   132       142  |    152       162       172       182       192       202       212       222       232       242  |    | -         -   |   272       282  
                                                     49-MSE                                                          114-MSE121  126                145-MSE                                                                                         241-MSE  250             266                  
                                                                                                                                                                                                                                                        245-MSE                                   


Chain D from PDB  Type:PROTEIN  Length:243
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:262
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
           T23O_XANCP    23 TYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV 284
               SCOP domains d1yw0d_ D: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------    ----------------------------------------------------------------------Trp_dioxygenase-1yw0D01 D:196-282                                                      -- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------    ----------------------------------------------------------------------Trp_dioxygenase-1yw0D02 D:196-282                                                      -- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------    ----------------------------------------------------------------------Trp_dioxygenase-1yw0D03 D:196-282                                                      -- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------    ----------------------------------------------------------------------Trp_dioxygenase-1yw0D04 D:196-282                                                      -- Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------    ----------------------------------------------------------------------Trp_dioxygenase-1yw0D05 D:196-282                                                      -- Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------    ----------------------------------------------------------------------Trp_dioxygenase-1yw0D06 D:196-282                                                      -- Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------    ----------------------------------------------------------------------Trp_dioxygenase-1yw0D07 D:196-282                                                      -- Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------    ----------------------------------------------------------------------Trp_dioxygenase-1yw0D08 D:196-282                                                      -- Pfam domains (8)
         Sec.struct. author hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh......----..hhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yw0 D  23 TYGGYLRLDQLLSAQQPLSEPAHHDEmLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYmGFRDVLG----FQSLQYRYIEFLLGNKNPQmLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHmRTVmRVIGF---------------ALALTFFPELFDVRTSVGV 284
                                    32        42      | 52        62        72        82        92       102       112 |      |-   |   132       142  |    152       162       172       182       192       202       212       222       232       242  |    | -         -   |   272       282  
                                                     49-MSE                                                          114-MSE121  126                145-MSE                                                                                         241-MSE  250             266                  
                                                                                                                                                                                                                                                        245-MSE
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YW0)

(-) 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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        T23O_XANCP | Q8PDA8: 2nw7 2nw8 2nw9 3bk9 3e08

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