1lrq: 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:1lrq.jpg|left|200px]]
- {{Structure
+==Aquifex aeolicus KDO8P synthase H185G mutant in complex with PEP, A5P and Cadmium==
-|PDB= 1lrq |SIZE=350|CAPTION= <scene name='initialview01'>1lrq</scene>, resolution 1.80&Aring;
+<StructureSection load='1lrq' size='340' side='right'caption='[[1lrq]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene> and <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>
+<table><tr><td colspan='2'>[[1lrq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LRQ FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1lrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrq OCA], [https://pdbe.org/1lrq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lrq RCSB], [https://www.ebi.ac.uk/pdbsum/1lrq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDSA_AQUAE KDSA_AQUAE]
+== 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/lr/1lrq_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=1lrq ConSurf].
+<div style="clear:both"></div>
-'''Aquifex aeolicus KDO8P synthase H185G mutant in complex with PEP, A5P and Cadmium'''
+==See Also==
+*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
+__TOC__
-==Overview==
+</StructureSection>
-Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) catalyzes the condensation of arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) by favoring the activation of a water molecule coordinated to the active-site metal ion. Cys11, His185, Glu222 and Asp233 are the other metal ligands. Wild-type KDO8PS is purified with Zn(2+) or Fe(2+) in the active site, but maximal activity in vitro is achieved when the endogenous metal is replaced with Cd(2+). The H185G enzyme retains 8% of the wild-type activity. ICP mass spectrometry analysis indicates that loss of His185 decreases the enzyme affinity for Fe(2+), but not for Zn(2+). However, maximal activity is again achieved by substitution of the endogenous metal with Cd(2+). We have determined the X-ray structures of the Cd(2+) H185G enzyme in its substrate-free form, and in complex with PEP, and PEP plus A5P. These structures show a normal amount of Cd(2+) bound, suggesting that coordination by His185 is not essential to retain Cd(2+) in the active site. Nonetheless, there are significant changes in the coordination sphere of Cd(2+) with respect to the wild-type enzyme, as the carboxylate moiety of PEP binds directly to the metal ion and replaces water and His185 as ligands. These observations indicate that the primary function of His185 in A.aeolicus KDO8PS is to orient PEP in the active site of the enzyme in such a way that a water molecule on the sinister (si) side of PEP can be activated by direct coordination to the metal ion.
-==About this Structure==
-LRQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRQ OCA].
-==Reference==
-Function of His185 in Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase., Wang J, Duewel HS, Stuckey JA, Woodard RW, Gatti DL, J Mol Biol. 2002 Nov 22;324(2):205-14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12441100 12441100]
-[[Category: 3-deoxy-8-phosphooctulonate synthase]]
 [[Category: Aquifex aeolicus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Duewel, H S.]]
+[[Category: Duewel HS]]
-[[Category: Gatti, D L.]]
+[[Category: Gatti DL]]
-[[Category: Stuckey, J A.]]
+[[Category: Stuckey JA]]
-[[Category: Wang, J.]]
+[[Category: Wang J]]
-[[Category: Woodard, R W.]]
+[[Category: Woodard RW]]
-[[Category: A5P]]
-[[Category: CD]]
-[[Category: PEP]]
-[[Category: PO4]]
-[[Category: kdo]]
-[[Category: kdo8p]]
-[[Category: kdo8p]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:34:23 2008''