1bg0: Difference between revisions

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-{{Seed}}
-[[Image:1bg0.png|left|200px]]
-<!--
+==TRANSITION STATE STRUCTURE OF ARGININE KINASE==
-The line below this paragraph, containing "STRUCTURE_1bg0", creates the "Structure Box" on the page.
+<StructureSection load='1bg0' size='340' side='right'caption='[[1bg0]], [[Resolution|resolution]] 1.86&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'>[[1bg0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Limulus_polyphemus Limulus polyphemus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BG0 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]] 1.86&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DAR:D-ARGININE'>DAR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-{{STRUCTURE_1bg0|  PDB=1bg0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bg0 OCA], [https://pdbe.org/1bg0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bg0 RCSB], [https://www.ebi.ac.uk/pdbsum/1bg0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bg0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KARG_LIMPO KARG_LIMPO]
+== 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/bg/1bg0_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=1bg0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Arginine kinase belongs to the family of enzymes, including creatine kinase, that catalyze the buffering of ATP in cells with fluctuating energy requirements and that has been a paradigm for classical enzymological studies. The 1.86-A resolution structure of its transition-state analog complex, reported here, reveals its active site and offers direct evidence for the importance of precise substrate alignment in the catalysis of bimolecular reactions, in contrast to the unimolecular reactions studied previously. In the transition-state analog complex studied here, a nitrate mimics the planar gamma-phosphoryl during associative in-line transfer between ATP and arginine. The active site is unperturbed, and the reactants are not constrained covalently as in a bisubstrate complex, so it is possible to measure how precisely they are pre-aligned by the enzyme. Alignment is exquisite. Entropic effects may contribute to catalysis, but the lone-pair orbitals are also aligned close enough to their optimal trajectories for orbital steering to be a factor during nucleophilic attack. The structure suggests that polarization, strain toward the transition state, and acid-base catalysis also contribute, but, in contrast to unimolecular enzyme reactions, their role appears to be secondary to substrate alignment in this bimolecular reaction.
-===TRANSITION STATE STRUCTURE OF ARGININE KINASE===
+Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions.,Zhou G, Somasundaram T, Blanc E, Parthasarathy G, Ellington WR, Chapman MS Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8449-54. PMID:9671698<ref>PMID:9671698</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1bg0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9671698}}, adds the Publication Abstract to the page
+*[[Arginine kinase|Arginine kinase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9671698 is the PubMed ID number.
+*[[Arginine kinase 3D structures|Arginine kinase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_9671698}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-BG0 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Limulus_polyphemus Limulus polyphemus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BG0 OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:9671698</ref><references group="xtra"/>
-[[Category: Arginine kinase]]
 [[Category: Limulus polyphemus]]
-[[Category: Blanc, E.]]
+[[Category: Blanc E]]
-[[Category: Chapman, M S.]]
+[[Category: Chapman MS]]
-[[Category: Ellington, W R.]]
+[[Category: Ellington WR]]
-[[Category: Parthasarathy, G.]]
+[[Category: Parthasarathy G]]
-[[Category: Somasundaram, T.]]
+[[Category: Somasundaram T]]
-[[Category: Zhou, G.]]
+[[Category: Zhou G]]
-[[Category: Adenosine triphosphate]]
-[[Category: Arginine kinase]]
-[[Category: Creatine kinase]]
-[[Category: Phosphagen kinase]]
-[[Category: Transferase]]
-[[Category: Transition state analog]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:39:37 2009''