1b9r: Difference between revisions

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-[[Image:1b9r.png|left|200px]]
-<!--
+==TERPREDOXIN FROM PSEUDOMONAS SP.==
-The line below this paragraph, containing "STRUCTURE_1b9r", creates the "Structure Box" on the page.
+<StructureSection load='1b9r' size='340' side='right'caption='[[1b9r]]' 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'>[[1b9r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B9R 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">Solution NMR</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
-{{STRUCTURE_1b9r|  PDB=1b9r  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b9r OCA], [https://pdbe.org/1b9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b9r RCSB], [https://www.ebi.ac.uk/pdbsum/1b9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b9r ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TERPB_PSESP TERPB_PSESP] The oxidation of alpha-terpineol by cytochrome p450-TERP requires the participation of a flavoprotein, terpredoxin reductase, and an iron-sulfur protein, terpredoxin, to mediate the transfer of electrons from NADH to P450 for oxygen activation.
+== 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/b9/1b9r_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=1b9r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Terpredoxin (Tdx) is a 105-residue bacterial ferredoxin consisting of a single polypeptide chain and a single Fe2S2 prosthetic group. Tdx was first identified in a strain of Pseudomonas sp. capable of using alpha-terpineol as sole carbon source. The Tdx gene, previously cloned from the plasmid-encoded terp operon, that carries genes encoding for proteins involved in terpineol catabolism, has been subcloned and expressed as the holoprotein in E. coli. Physical characterization of the expressed Tdx has been performed, and a model for the solution structure of oxidized Tdx (Tdxo) has been determined. High-resolution homo- and heteronuclear NMR data have been used for structure determination in diamagnetic regions of the protein. The structure of the metal binding site (which cannot be determined directly by NMR methods due to paramagnetic broadening of resonances) was modeled using restraints obtained from a crystal structure of the homologous ferredoxin adrenodoxin (Adx) and loose restraints determined from paramagnetic broadening patterns in NMR spectra. Essentially complete 1H and 15N NMR resonance assignments have been made for the diamagnetic region of Tdxo (ca. 80% of the protein). A large five-stranded beta-sheet and a smaller two-stranded beta-sheet were identified, along with three alpha-helices. A high degree of structural homology was observed between Tdx and two other ferredoxins with sequence and functional homology to Tdx for which structures have been determined, Adx and putidaredoxin (Pdx), a homologous Pseudomonas protein. 1H/2H exchange rates for Tdx backbone NH groups were measured for both oxidation states and are rationalized in the context of the Tdx structure. In particular, an argument is made for the importance of the residue following the third ligand of the metal cluster (Arg49 in Tdx, His49 in Pdx, His56 in Adx) in modulating protein dynamics as a function of oxidation state. Some differences between Tdx and Pdx are detected by UV-visible spectroscopy, and structural differences at the C-terminal region were also observed. Tdx exhibits only 2% of the activity of Pdx in turnover assays performed using the reconstituted camphor hydroxylase system of which Pdx is the natural component.
-===TERPREDOXIN FROM PSEUDOMONAS SP.===
+A model for the solution structure of oxidized terpredoxin, a Fe2S2 ferredoxin from Pseudomonas.,Mo H, Pochapsky SS, Pochapsky TC Biochemistry. 1999 Apr 27;38(17):5666-75. PMID:10220356<ref>PMID:10220356</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_10220356}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1b9r" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 10220356 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_10220356}}
-==About this Structure==
-[[1b9r]] is a 1 chain structure of [[Ferredoxin]] with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B9R OCA].
 ==See Also==
-*[[Ferredoxin]]
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:10220356</ref><references group="xtra"/>
+__TOC__
-[[Category: Pseudomonas sp.]]
+</StructureSection>
-[[Category: Mo, H.]]
+[[Category: Large Structures]]
-[[Category: Pochapsky, S S.]]
+[[Category: Pseudomonas sp]]
-[[Category: Pochapsky, T C.]]
+[[Category: Mo H]]
-[[Category: Ferredoxin]]
+[[Category: Pochapsky SS]]
-[[Category: Structure from molmol]]
+[[Category: Pochapsky TC]]