1cib: Difference between revisions

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-[[Image:1cib.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1cib", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1cib|  PDB=1cib  |  SCENE=  }}
-'''STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM E. COLI COMPLEXED WITH GDP, IMP, HADACIDIN, AND NO3'''
+==STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM E. COLI COMPLEXED WITH GDP, IMP, HADACIDIN, AND NO3==
+<StructureSection load='1cib' size='340' side='right'caption='[[1cib]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1cib]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CIB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CIB FirstGlance]. <br>
+</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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=HDA:HADACIDIN'>HDA</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=1cib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cib OCA], [https://pdbe.org/1cib PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cib RCSB], [https://www.ebi.ac.uk/pdbsum/1cib PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cib ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PURA_ECOLI PURA_ECOLI] Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP (By similarity).[HAMAP-Rule:MF_00011]
+== 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/ci/1cib_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=1cib ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Guanosine 5'-diphosphate 3'-diphosphate (ppGpp), a pleiotropic effector of the stringent response, potently inhibits adenylosuccinate synthetase from Escherichia coli as an allosteric effector and/or as a competitive inhibitor with respect to GTP. Crystals of the synthetase grown in the presence of IMP, hadacidin, NO3-, and Mg2+, then soaked with ppGpp, reveal electron density at the GTP pocket which is consistent with guanosine 5'-diphosphate 2':3'-cyclic monophosphate. Unlike ligand complexes of the synthetase involving IMP and GDP, the coordination of Mg2+ in this complex is octahedral with the side chain of Asp13 in the inner sphere of the cation. The cyclic phosphoryl group interacts directly with the side chain of Lys49 and indirectly through bridging water molecules with the side chains of Asn295 and Arg305. The synthetase either directly facilitates the formation of the cyclic nucleotide or scavenges trace amounts of the cyclic nucleotide from solution. Regardless of its mode of generation, the cyclic nucleotide binds far more tightly to the active site than does ppGpp. Conceivably, synthetase activity in vivo during the stringent response may be sensitive to the relative concentrations of several effectors, which together exercise precise control over the de novo synthesis of AMP.
-==Overview==
+Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase.,Hou Z, Cashel M, Fromm HJ, Honzatko RB J Biol Chem. 1999 Jun 18;274(25):17505-10. PMID:10364182<ref>PMID:10364182</ref>
-Guanosine 5'-diphosphate 3'-diphosphate (ppGpp), a pleiotropic effector of the stringent response, potently inhibits adenylosuccinate synthetase from Escherichia coli as an allosteric effector and/or as a competitive inhibitor with respect to GTP. Crystals of the synthetase grown in the presence of IMP, hadacidin, NO3-, and Mg2+, then soaked with ppGpp, reveal electron density at the GTP pocket which is consistent with guanosine 5'-diphosphate 2':3'-cyclic monophosphate. Unlike ligand complexes of the synthetase involving IMP and GDP, the coordination of Mg2+ in this complex is octahedral with the side chain of Asp13 in the inner sphere of the cation. The cyclic phosphoryl group interacts directly with the side chain of Lys49 and indirectly through bridging water molecules with the side chains of Asn295 and Arg305. The synthetase either directly facilitates the formation of the cyclic nucleotide or scavenges trace amounts of the cyclic nucleotide from solution. Regardless of its mode of generation, the cyclic nucleotide binds far more tightly to the active site than does ppGpp. Conceivably, synthetase activity in vivo during the stringent response may be sensitive to the relative concentrations of several effectors, which together exercise precise control over the de novo synthesis of AMP.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-CIB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CIB OCA].
+</div>
+<div class="pdbe-citations 1cib" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase., Hou Z, Cashel M, Fromm HJ, Honzatko RB, J Biol Chem. 1999 Jun 18;274(25):17505-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10364182 10364182]
+*[[Adenylosuccinate synthetase 3D structures|Adenylosuccinate synthetase 3D structures]]
-[[Category: Adenylosuccinate synthase]]
+== References ==
-[[Category: Escherichia coli]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Cashel, M.]]
+</StructureSection>
-[[Category: Fromm, H J.]]
+[[Category: Escherichia coli K-12]]
-[[Category: Honzatko, R B.]]
+[[Category: Large Structures]]
-[[Category: Hou, Z.]]
+[[Category: Cashel M]]
-[[Category: Gdp]]
+[[Category: Fromm HJ]]
-[[Category: Gtp-hydrolysing enzyme]]
+[[Category: Honzatko RB]]
-[[Category: Ligase]]
+[[Category: Hou Z]]
-[[Category: Purine 2 nucleotide biosynthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 12:45:44 2008''