1nf2: Difference between revisions

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-[[Image:1nf2.gif|left|200px]]
- {{Structure
+==X-ray crystal structure of TM0651 from Thermotoga maritima==
-|PDB= 1nf2 |SIZE=350|CAPTION= <scene name='initialview01'>1nf2</scene>, resolution 2.20&Aring;
+<StructureSection load='1nf2' size='340' side='right'caption='[[1nf2]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[1nf2]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NF2 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam08282 Hydrolase_3]</span>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nf2 OCA], [https://pdbe.org/1nf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nf2 RCSB], [https://www.ebi.ac.uk/pdbsum/1nf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nf2 ProSAT], [https://www.topsan.org/Proteins/BSGC/1nf2 TOPSAN]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nf2 OCA], [http://www.ebi.ac.uk/pdbsum/1nf2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nf2 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/Q9WZB9_THEMA Q9WZB9_THEMA]
+== Evolutionary Conservation ==
-'''X-ray crystal structure of TM0651 from Thermotoga maritima'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nf/1nf2_consurf.spt"</scriptWhenChecked>
-We have determined the crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima, TM0651 (gi 4981173), at 2.2 A resolution by selenomethionine single-wavelength anomalous diffraction (SAD) techniques. TM0651 is a member of the haloacid dehalogenase (HAD) superfamily, with sequence homology to trehalose-6-phosphate phosphatase and sucrose-6(F)-phosphate phosphohydrolase. Selenomethionine labeled TM0651 crystallized in space group C2 with three monomers per asymmetric unit. Each monomer has approximate dimensions of 65 x 40 x 35 A(3), and contains two domains: a domain of known hydrolase fold characteristic of the HAD family, and a domain with a new tertiary fold consisting of a six-stranded beta-sheet surrounded by four alpha-helices. There is one disulfide bond between residues Cys35 and Cys265 in each monomer. One magnesium ion and one sulfate ion are bound in the active site. The superposition of active site residues with other HAD family members indicates that TM0651 is very likely a phosphatase that acts through the formation of a phosphoaspartate intermediate, which is supported by both NMR titration data and a biochemical assay. Structural and functional database searches and the presence of many aromatic residues in the interface of the two domains suggest the substrate of TM0651 is a carbohydrate molecule. From the crystal structure and NMR data, the protein likely undergoes a conformational change upon substrate binding.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-NF2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NF2 OCA].
+</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=1nf2 ConSurf].
+<div style="clear:both"></div>
-==Reference==
+__TOC__
-Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima., Shin DH, Roberts A, Jancarik J, Yokota H, Kim R, Wemmer DE, Kim SH, Protein Sci. 2003 Jul;12(7):1464-72. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12824492 12824492]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Large Structures]]
 [[Category: Thermotoga maritima]]
-[[Category: BSGC, Berkeley Structural Genomics Center.]]
+[[Category: Shin DH]]
-[[Category: Shin, D H.]]
-[[Category: berkeley structural genomics center]]
-[[Category: bsgc structure funded by nih]]
-[[Category: had family]]
-[[Category: new fold]]
-[[Category: phosphatase]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: structural genomic]]
-[[Category: structural proteomic]]
-[[Category: thermotoga maritima]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:29:28 2008''