2NW8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF TRYPTOPHAN 2,3-DIOXYGENASE (TDO) FROM XANTHOMONAS CAMPESTRIS IN COMPLEX WITH FERROUS HEME AND TRYPTOPHAN. NORTHEAST STRUCTURAL GENOMICS TARGET XCR13.

Authors :   F. Forouhar, J. L. R. Anderson, C. G. Mowat, C. Bruckmann, S. J. Thackray J. Seetharaman, C. K. Ho, L. C. Ma, K. Cunningham, H. Janjua, L. Zhao, R. J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, S. K. Champma Northeast Structural Genomics Consortium (Nesg)

Date :   14 Nov 06 (Deposition) - 19 Dec 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

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

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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	TRP	4	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	TRP	8	Mod. Amino Acid	TRYPTOPHAN

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:491 , HOH B:497 , HOH B:500 , HOH B:574 , HOH B:744 , HOH B:752	BINDING SITE FOR RESIDUE MN B 307
2	AC2	SOFTWARE	GLU B:207 , HOH B:524 , HOH B:551 , HOH B:564 , HOH B:596 , HOH B:764	BINDING SITE FOR RESIDUE MN B 308
3	AC3	SOFTWARE	PHE A:51 , HIS A:55 , TYR A:113 , ARG A:117 , SER A:123 , GLY A:253 , THR A:254 , HEM A:401 , HOH A:402 , TYR B:24	BINDING SITE FOR RESIDUE TRP A 307
4	AC4	SOFTWARE	ARG A:85 , LYS A:92 , TYR A:220 , SER A:221 , GLU A:224 , ASP A:228 , HOH A:411 , HOH A:422 , HOH A:442 , HOH A:502 , HOH A:698 , LYS B:86 , ALA B:89 , HOH B:536 , HOH B:597	BINDING SITE FOR RESIDUE TRP A 308
5	AC5	SOFTWARE	TYR A:24 , ARG A:215 , PHE B:51 , HIS B:55 , TYR B:113 , GLY B:121 , PRO B:122 , SER B:123 , HOH B:402 , HOH B:687	BINDING SITE FOR RESIDUE TRP B 309
6	AC6	SOFTWARE	LYS A:86 , ALA A:89 , HOH A:495 , HOH A:539 , ARG B:85 , LYS B:92 , TYR B:220 , SER B:221 , GLU B:224 , ASP B:225 , ASP B:228 , HOH B:411 , HOH B:434 , HOH B:517 , HOH B:560	BINDING SITE FOR RESIDUE TRP B 310
7	AC7	SOFTWARE	PHE A:51 , GLN A:54 , HIS A:55 , SER A:58 , TRP A:102 , LEU A:105 , SER A:124 , GLY A:125 , PHE A:126 , TYR A:131 , ARG A:132 , HIS A:240 , VAL A:244 , ILE A:248 , GLY A:253 , THR A:254 , GLY A:255 , GLY A:256 , SER A:257 , GLY A:259 , TRP A:307 , HOH A:402 , HOH A:459 , HOH A:514 , HOH A:534 , HOH A:694 , TYR B:24	BINDING SITE FOR RESIDUE HEM A 401
8	AC8	SOFTWARE	TYR A:24 , ARG A:215 , PHE B:51 , GLN B:54 , HIS B:55 , SER B:58 , TRP B:102 , SER B:124 , GLY B:125 , PHE B:126 , TYR B:131 , ARG B:132 , HIS B:240 , VAL B:244 , ILE B:248 , GLY B:259 , HOH B:402 , HOH B:489 , HOH B:499 , HOH B:741 , HOH B:751	BINDING SITE FOR RESIDUE HEM B 401

(no "SS Bond" information available for 2NW8)

Asymmetric Unit

No.	Residues
1	Glu A:42	-	Pro A:43
2	Glu B:42	-	Pro B:43

(no "SAP(SNP)/Variant" information available for 2NW8)

(no "PROSITE Motif" information available for 2NW8)

(no "Exon" information available for 2NW8)

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:268
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:280
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298
           T23O_XANCP    19 EGRLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGVDNRPPQGSADAGKR 298
               SCOP domains d2nw8a_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh....hhhhhhhhhh...------------.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nw8 A  19 EGRLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGV------------WW 308
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278     |   -       308
                                                                                                                                                                                                                                                                                                   284          307

Chain B from PDB  Type:PROTEIN  Length:264
 aligned with T23O_XANCP | Q8PDA8 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:270
                                    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       290
           T23O_XANCP    21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGVDNRPPQ 290
               SCOP domains d2nw8b_ B: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw8B01 B:196-282                                                      -------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw8B02 B:196-282                                                      -------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw8B03 B:196-282                                                      -------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Trp_dioxygenase-2nw8B04 B:196-282                                                      -------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhh.........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------.hhhhhhhhhh....hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nw8 B  21 RLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGF------SSGVGFLQQALALTFFPELFDVRTSVGVDNRPPQ 290
                                    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       290
                                                                                                                                                                                                                                                               250    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 '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Indolic compounds 2,3-dioxygenase-like (13)

Superfamily: Indolic compounds 2,3-dioxygenase-like (13)

Family: automated matches (6)

Protein domain: automated matches (6)

Xanthomonas campestris [TaxId: 340] (5)

1a	d2nw8a_	A:
1b	d2nw8b_	B:

(no "CATH Domain" information available for 2NW8)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: IDO-like (6)

Family: Trp_dioxygenase (4)

Xanthomonas campestris pv. campestris (4)

1a	Trp_dioxygenase-2nw8B01	B:196-282
1b	Trp_dioxygenase-2nw8B02	B:196-282
1c	Trp_dioxygenase-2nw8B03	B:196-282
1d	Trp_dioxygenase-2nw8B04	B:196-282

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:42 - Pro A:43	[ RasMol ]
		Glu B:42 - Pro B:43	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	2nw8
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UniProtKB/Swiss-Prot
	T23O_XANCP \| Q8PDA8	:	1yw0 2nw7 2nw9 3bk9 3e08

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

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Pfam Domains (1, 4)

Gene Ontology (10, 10)

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