1tb3: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1tb3.png|left|200px]]
-<!--
+==Crystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid Oxidase==
-The line below this paragraph, containing "STRUCTURE_1tb3", creates the "Structure Box" on the page.
+<StructureSection load='1tb3' size='340' side='right'caption='[[1tb3]], [[Resolution|resolution]] 2.30&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'>[[1tb3]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TB3 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-{{STRUCTURE_1tb3|  PDB=1tb3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tb3 OCA], [https://pdbe.org/1tb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tb3 RCSB], [https://www.ebi.ac.uk/pdbsum/1tb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tb3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HAOX2_RAT HAOX2_RAT] Catalyzes the oxidation of L-alpha-hydroxy acids as well as, more slowly, that of L-alpha-amino acids.
+== 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/tb/1tb3_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=1tb3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Long chain hydroxy acid oxidase (LCHAO) is a member of an FMN-dependent enzyme family that oxidizes L-2-hydroxy acids to ketoacids. LCHAO is a peroxisomal enzyme, and the identity of its physiological substrate is unclear. Mandelate is the most efficient substrate known and is commonly used in the test tube. LCHAO differs from most family members in that one of the otherwise invariant active site residues is a phenylalanine (Phe23) instead of a tyrosine. We now report the crystal structure of LCHAO. It shows the same beta8alpha8 TIM barrel structure as other structurally characterized family members, e.g., spinach glycolate oxidase (GOX) and the electron transferases yeast flavocytochrome b2 (FCB2) and Pseudomonas putida mandelate dehydrogenase (MDH). Loop 4, which is mobile in other family members, is visible in part. An acetate ion is present in the active site. The flavin interacts with the protein in the same way as in the electron transferases, and not as in GOX, an unexpected observation. An interpretation is proposed to explain this difference between GOX on one hand and FCB2 and LCHAO on the other hand, which had been proposed to arise from the differences between family members in their reactivity with oxygen. A comparison of models of the substrate bound to various published structures suggests that the very different reactivity with mandelate of LCHAO, GOX, FCB2, and MDH cannot be rationalized by a hydride transfer mechanism.
-===Crystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid Oxidase===
+Crystal structure analysis of recombinant rat kidney long chain hydroxy acid oxidase.,Cunane LM, Barton JD, Chen ZW, Le KH, Amar D, Lederer F, Mathews FS Biochemistry. 2005 Feb 8;44(5):1521-31. PMID:15683236<ref>PMID:15683236</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1tb3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15683236}}, adds the Publication Abstract to the page
+*[[Glycolate oxidase 3D structures|Glycolate oxidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15683236 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15683236}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-TB3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TB3 OCA].
-==Reference==
-Crystal structure analysis of recombinant rat kidney long chain hydroxy acid oxidase., Cunane LM, Barton JD, Chen ZW, Le KH, Amar D, Lederer F, Mathews FS, Biochemistry. 2005 Feb 8;44(5):1521-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15683236 15683236]
-Refined structure of spinach glycolate oxidase at 2 A resolution., Lindqvist Y, J Mol Biol. 1989 Sep 5;209(1):151-66. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2681790 2681790]
-Molecular structure of flavocytochrome b2 at 2.4 A resolution., Xia ZX, Mathews FS, J Mol Biol. 1990 Apr 20;212(4):837-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2329585 2329585]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Amar D]]
-[[Category: Amar, D.]]
+[[Category: Barton JD]]
-[[Category: Barton, J D.]]
+[[Category: Chen ZW]]
-[[Category: Chen, Z W.]]
+[[Category: Cunane LM]]
-[[Category: Cunane, L M.]]
+[[Category: Le KHD]]
-[[Category: Le, K H.D.]]
+[[Category: Lederer F]]
-[[Category: Lederer, F.]]
+[[Category: Mathews FS]]
-[[Category: Mathews, F S.]]
-[[Category: Flavoprotein]]
-[[Category: Long chain alpha-hydroxy acid oxidase]]
-[[Category: Oxidase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 20:04:10 2008''