1aja: 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:1aja.jpg|left|200px]]
-<!--
+==THREE-DIMENSIONAL STRUCTURE OF THE D153G MUTANT OF E. COLI ALKALINE PHOSPHATASE: A MUTANT WITH WEAKER MAGNESIUM BINDING AND INCREASED CATALYTIC ACTIVITY==
-The line below this paragraph, containing "STRUCTURE_1aja", creates the "Structure Box" on the page.
+<StructureSection load='1aja' size='340' side='right'caption='[[1aja]], [[Resolution|resolution]] 2.50&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'>[[1aja]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AJA 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]] 2.5&#8491;</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=1aja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aja OCA], [https://pdbe.org/1aja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aja RCSB], [https://www.ebi.ac.uk/pdbsum/1aja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aja ProSAT]</span></td></tr>
-{{STRUCTURE_1aja|  PDB=1aja  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PPB_ECOLI PPB_ECOLI]
+== 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/aj/1aja_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=1aja ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Here we present the refined crystal structures of three different conformational states of the Asp153--&gt;Gly mutant (D153G) of alkaline phosphatase (AP), a metalloenzyme from Escherichia coli. The apo state is induced in the crystal over a 3 month period by metal depletion of the holoenzyme crystals. Subsequently, the metals are reintroduced in the crystalline state in a time-dependent reversible manner without physically damaging the crystals. Two structural intermediates of the holo form based on data from a 2 week (intermediate I) and a 2 month soak (intermediate II) of the apo crystals with Mg2+ and Zn2+ have been identified. The three-dimensional crystal structures of the apo (R = 18.1%), intermediate I (R = 19.5%), and intermediate II (R = 19.9%) of the D153G enzyme have been refined and the corresponding structures analyzed and compared. Large conformational changes that extend from the mutant active site to surface loops, located 20 A away, are observed in the apo structure with respect to the holo structure. The structure of intermediate I shows the recovery of the entire enzyme to an almost native-like conformation, with the exception of residues Asp 51 and Asp 369 in the active site and the surface loop (406-410) which remains partially disordered. In the three-dimensional structure of intermediate II, both Asp 51 and Asp 369 are essentially in a native-like conformation, but the main chain of residues 406-408 within the loop is still not fully ordered. The D153G mutant protein exhibits weak, reversible, time dependent metal binding in solution and in the crystalline state.(ABSTRACT TRUNCATED AT 250 WORDS)
-'''THREE-DIMENSIONAL STRUCTURE OF THE D153G MUTANT OF E. COLI ALKALINE PHOSPHATASE: A MUTANT WITH WEAKER MAGNESIUM BINDING AND INCREASED CATALYTIC ACTIVITY'''
+Crystallographic analysis of reversible metal binding observed in a mutant (Asp153--&gt;Gly) of Escherichia coli alkaline phosphatase.,Dealwis CG, Brennan C, Christianson K, Mandecki W, Abad-Zapatero C Biochemistry. 1995 Oct 31;34(43):13967-73. PMID:7577993<ref>PMID:7577993</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1aja" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The substitution of aspartate at position 153 in Escherichia coli alkaline phosphatase by glycine results in a mutant enzyme with 5-fold higher catalytic activity (kcat) but no change in Km at pH 8.0 in 50 mM Tris-HCl. The increased kcat is achieved by a faster release of the phosphate product as a result of the lower phosphate affinity. The mutation also affects Mg2+ binding, resulting in an enzyme with lower metal affinity. The 3-D X-ray structure of the D153G mutant has been refined at 2.5 A to a crystallographic R-factor of 16.2%. An analysis of this structure has revealed that the decreased phosphate affinity is caused by an apparent increase in flexibility of the guanidinium side chain of Arg166 involved in phosphate binding. The mutation of Asp153 to Gly also affects the position of the water ligands of Mg2+, and the loop Gln152-Thr155 is shifted by 0.3 A away from the active site. The weaker Mg2+ binding of the mutant compared with the wild type is caused by an altered coordination sphere in the proximity of the Mg2+ ion, and also by the loss of an electrostatic interaction (Mg2+.COO-Asp153) in the mutant. Its ligands W454 and W455 and hydroxyl of Thr155, involved in the octahedral coordination of the Mg2+ ion, are further apart in the mutant compared with the wild type.
+*[[Alkaline phosphatase 3D structures|Alkaline phosphatase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-AJA 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=1AJA OCA].
+__TOC__
+</StructureSection>
-==Reference==
--D structure of the D153G mutant of Escherichia coli alkaline phosphatase: an enzyme with weaker magnesium binding and increased catalytic activity., Dealwis CG, Chen L, Brennan C, Mandecki W, Abad-Zapatero C, Protein Eng. 1995 Sep;8(9):865-71. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8746724 8746724]
-[[Category: Alkaline phosphatase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Abad-Zapatero, C.]]
+[[Category: Abad-Zapatero C]]
-[[Category: Chen, L.]]
+[[Category: Chen L]]
-[[Category: Dealwis, C G.]]
+[[Category: Dealwis CG]]
-[[Category: Non specific mono-esterase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 10:20:37 2008''