1pdz: 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: @@
-[[Image:1pdz.jpg|left|200px]]
- {{Structure
+==X-RAY STRUCTURE AND CATALYTIC MECHANISM OF LOBSTER ENOLASE==
-|PDB= 1pdz |SIZE=350|CAPTION= <scene name='initialview01'>1pdz</scene>, resolution 2.2&Aring;
+<StructureSection load='1pdz' size='340' side='right'caption='[[1pdz]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> and <scene name='pdbligand=ACE:ACETYL GROUP'>ACE</scene>
+<table><tr><td colspan='2'>[[1pdz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homarus_gammarus Homarus gammarus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PDZ FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Phosphopyruvate_hydratase Phosphopyruvate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.11 4.2.1.11]
+</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=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
-}}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pdz OCA], [https://pdbe.org/1pdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pdz RCSB], [https://www.ebi.ac.uk/pdbsum/1pdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pdz ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ENO_HOMGA ENO_HOMGA]
+== 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/pd/1pdz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1pdz ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Enolase prepared from lobster tail muscle yielded trigonal crystals with one 47 kDa subunit per asymmetric unit. X-ray data were collected on the apoenzyme at 2.4 A resolution and on a complex with Mn2+ and the inhibitor phosphoglycolate at 2.2 A resolution. The corresponding cDNA was amplified from a library of lobster muscle cDNA, and a sequence corresponding to residues 27-398 was determined. It is highly homologous to other enolases, including yeast enolase for which an X-ray structure is available. Yeast enolase was used as a starting point for crystallographic refinement, which led to models of lobster enolase having R-factors below 22% and good stereochemistry. These models are very similar to yeast enolase; they have the same fold with a beta 3 alpha 4 N-terminal domain followed by an atypical alpha/beta barrel. Lobster apoenolase and the ternary complex differ only in the position of three mobile loops. In the complex, a single Mn2+ ion is seen ligated to three carboxylates and three water molecules. Phosphoglycolate binds near, but not directly to, the metal. His 157, which belongs to one of the mobile loops, is in contact with the C2 atom of the ligand. A water molecule hydrogen-bonds to the carboxylate of the ligand and to those of Glu 166 and Glu 209. We suggest that His 157 is the base that abstracts the C2H proton, whereas the water molecule is part of a proton relay system keeping the substrate in the carboxylic acid form where the pKa of the C2H group is low enough for proton transfer to His 157. The resulting catalytic mechanism is different from those proposed on the basis of the yeast enzyme X-ray structures, but it fits with earlier biochemical and spectroscopic data.
-'''X-RAY STRUCTURE AND CATALYTIC MECHANISM OF LOBSTER ENOLASE'''
+X-ray structure and catalytic mechanism of lobster enolase.,Duquerroy S, Camus C, Janin J Biochemistry. 1995 Oct 3;34(39):12513-23. PMID:7547999<ref>PMID:7547999</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1pdz" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Enolase prepared from lobster tail muscle yielded trigonal crystals with one 47 kDa subunit per asymmetric unit. X-ray data were collected on the apoenzyme at 2.4 A resolution and on a complex with Mn2+ and the inhibitor phosphoglycolate at 2.2 A resolution. The corresponding cDNA was amplified from a library of lobster muscle cDNA, and a sequence corresponding to residues 27-398 was determined. It is highly homologous to other enolases, including yeast enolase for which an X-ray structure is available. Yeast enolase was used as a starting point for crystallographic refinement, which led to models of lobster enolase having R-factors below 22% and good stereochemistry. These models are very similar to yeast enolase; they have the same fold with a beta 3 alpha 4 N-terminal domain followed by an atypical alpha/beta barrel. Lobster apoenolase and the ternary complex differ only in the position of three mobile loops. In the complex, a single Mn2+ ion is seen ligated to three carboxylates and three water molecules. Phosphoglycolate binds near, but not directly to, the metal. His 157, which belongs to one of the mobile loops, is in contact with the C2 atom of the ligand. A water molecule hydrogen-bonds to the carboxylate of the ligand and to those of Glu 166 and Glu 209. We suggest that His 157 is the base that abstracts the C2H proton, whereas the water molecule is part of a proton relay system keeping the substrate in the carboxylic acid form where the pKa of the C2H group is low enough for proton transfer to His 157. The resulting catalytic mechanism is different from those proposed on the basis of the yeast enzyme X-ray structures, but it fits with earlier biochemical and spectroscopic data.
+*[[Enolase 3D structures|Enolase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-PDZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homarus_gammarus Homarus gammarus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDZ OCA].
+__TOC__
+</StructureSection>
-==Reference==
-X-ray structure and catalytic mechanism of lobster enolase., Duquerroy S, Camus C, Janin J, Biochemistry. 1995 Oct 3;34(39):12513-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7547999 7547999]
 [[Category: Homarus gammarus]]
-[[Category: Phosphopyruvate hydratase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Camus C]]
-[[Category: Bras, G Le.]]
+[[Category: Duquerroy S]]
-[[Category: Camus, C.]]
+[[Category: Janin J]]
-[[Category: Duquerroy, S.]]
+[[Category: Le Bras G]]
-[[Category: Janin, J.]]
-[[Category: ACE]]
-[[Category: MN]]
-[[Category: PGA]]
-[[Category: lyase (carbon-oxygen)]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:23:11 2008''