2nw9: Difference between revisions

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-{{Seed}}
-[[Image:2nw9.png|left|200px]]
-<!--
+==Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferrous heme and 6-fluoro-tryptophan. Northeast Structural Genomics Target XcR13==
-The line below this paragraph, containing "STRUCTURE_2nw9", creates the "Structure Box" on the page.
+<StructureSection load='2nw9' size='340' side='right'caption='[[2nw9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2nw9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NW9 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FT6:6-FLUORO-L-TRYPTOPHAN'>FT6</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-{{STRUCTURE_2nw9|  PDB=2nw9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nw9 OCA], [https://pdbe.org/2nw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nw9 RCSB], [https://www.ebi.ac.uk/pdbsum/2nw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nw9 ProSAT], [https://www.topsan.org/Proteins/NESGC/2nw9 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/T23O_XANCP T23O_XANCP] Catalyzes the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring.[HAMAP-Rule:MF_01972]<ref>PMID:17197414</ref> <ref>PMID:18783250</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nw/2nw9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2nw9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. Here, we report extensive structural and biochemical studies of the Xanthomonas campestris TDO and a related protein SO4414 from Shewanella oneidensis, including the structure at 1.6-A resolution of the catalytically active, ferrous form of TDO in a binary complex with the substrate L-Trp. The carboxylate and ammonium moieties of tryptophan are recognized by electrostatic and hydrogen-bonding interactions with the enzyme and a propionate group of the heme, thus defining the L-stereospecificity. A second, possibly allosteric, L-Trp-binding site is present at the tetramer interface. The sixth coordination site of the heme-iron is vacant, providing a dioxygen-binding site that would also involve interactions with the ammonium moiety of L-Trp and the amide nitrogen of a glycine residue. The indole ring is positioned correctly for oxygenation at the C2 and C3 atoms. The active site is fully formed only in the binary complex, and biochemical experiments confirm this induced-fit behavior of the enzyme. The active site is completely devoid of water during catalysis, which is supported by our electrochemical studies showing significant stabilization of the enzyme upon substrate binding.
-===Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferrous heme and 6-fluoro-tryptophan. Northeast Structural Genomics Target XcR13===
+Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase.,Forouhar F, Anderson JL, Mowat CG, Vorobiev SM, Hussain A, Abashidze M, Bruckmann C, Thackray SJ, Seetharaman J, Tucker T, Xiao R, Ma LC, Zhao L, Acton TB, Montelione GT, Chapman SK, Tong L Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):473-8. Epub 2006 Dec 29. PMID:17197414<ref>PMID:17197414</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2nw9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17197414}}, adds the Publication Abstract to the page
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17197414 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17197414}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-NW9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NW9 OCA].
-==Reference==
-Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase., Forouhar F, Anderson JL, Mowat CG, Vorobiev SM, Hussain A, Abashidze M, Bruckmann C, Thackray SJ, Seetharaman J, Tucker T, Xiao R, Ma LC, Zhao L, Acton TB, Montelione GT, Chapman SK, Tong L, Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):473-8. Epub 2006 Dec 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17197414 17197414]
-[[Category: Single protein]]
 [[Category: Xanthomonas campestris pv. campestris]]
-[[Category: Acton, T B.]]
+[[Category: Acton TB]]
-[[Category: Anderson, J L.R.]]
+[[Category: Anderson JLR]]
-[[Category: Baran, M C.]]
+[[Category: Baran MC]]
-[[Category: Bruckmann, C.]]
+[[Category: Bruckmann C]]
-[[Category: Champman, S K.]]
+[[Category: Champman SK]]
-[[Category: Cunningham, K.]]
+[[Category: Cunningham K]]
-[[Category: Forouhar, F.]]
+[[Category: Forouhar F]]
-[[Category: Ho, C K.]]
+[[Category: Ho CK]]
-[[Category: Janjua, H.]]
+[[Category: Janjua H]]
-[[Category: Liu, J.]]
+[[Category: Liu J]]
-[[Category: Ma, L C.]]
+[[Category: Ma LC]]
-[[Category: Montelione, G T.]]
+[[Category: Montelione GT]]
-[[Category: Mowat, C G.]]
+[[Category: Mowat CG]]
-[[Category: NESG, Northeast Structural Genomics Consortium.]]
+[[Category: Rost B]]
-[[Category: Rost, B.]]
+[[Category: Seetharaman J]]
-[[Category: Seetharaman, J.]]
+[[Category: Thackray SJ]]
-[[Category: Thackray, S J.]]
+[[Category: Tong L]]
-[[Category: Tong, L.]]
+[[Category: Xiao R]]
-[[Category: Xiao, R.]]
+[[Category: Zhao L]]
-[[Category: Zhao, L.]]
-[[Category: All alpha-helical protein]]
-[[Category: Nesg]]
-[[Category: Northeast structural genomics consortium]]
-[[Category: Protein structure initiative]]
-[[Category: Psi-2]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 16:12:20 2008''