1ez1: Difference between revisions

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-[[Image:1ez1.jpg|left|200px]]<br /><applet load="1ez1" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ez1, resolution 1.75&Aring;" />
-'''STRUCTURE OF ESCHERICHIA COLI PURT-ENCODED GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE COMPLEXED WITH MG, AMPPNP, AND GAR'''<br />
-==Overview==
+==STRUCTURE OF ESCHERICHIA COLI PURT-ENCODED GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE COMPLEXED WITH MG, AMPPNP, AND GAR==
-In Escherichia coli, the PurT-encoded glycinamide ribonucleotide, transformylase, or PurT transformylase, catalyzes an alternative, formylation of glycinamide ribonucleotide (GAR) in the de novo pathway for, purine biosynthesis. On the basis of amino acid sequence analyses, it is, known that the PurT transformylase belongs to the ATP-grasp superfamily of, proteins. The common theme among members of this superfamily is a, catalytic reaction mechanism that requires ATP and proceeds through an, acyl phosphate intermediate. All of the enzymes belonging to the ATP-grasp, superfamily are composed of three structural motifs, termed the A-, B-, and C-domains, and in each case, the ATP is wedged between the B- and, C-domains. Here we describe two high-resolution X-ray crystallographic, structures of PurT transformylase from E. coli: one form complexed with, the nonhydrolyzable ATP analogue AMPPNP and the second with bound AMPPNP, and GAR. The latter structure is of special significance because it, represents the first ternary complex to be determined for a member of the, ATP-grasp superfamily involved in purine biosynthesis and as such provides, new information about the active site region involved in ribonucleotide, binding. Specifically in PurT transformylase, the GAR substrate is, anchored to the protein via Glu 82, Asp 286, Lys 355, Arg 362, and Arg, 363. Key amino acid side chains involved in binding the AMPPNP to the, enzyme include Arg 114, Lys 155, Glu 195, Glu 203, and Glu 267., Strikingly, the amino group of GAR that is formylated during the reaction, lies at 2.8 A from one of the gamma-phosphoryl oxygens of the AMPPNP.
+<StructureSection load='1ez1' size='340' side='right'caption='[[1ez1]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1ez1]] 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=1EZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EZ1 FirstGlance]. <br>
-EZ1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG, ACT, NA, ANP, GAR and MPO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EZ1 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GAR:GLYCINAMIDE+RIBONUCLEOTIDE'>GAR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ez1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ez1 OCA], [https://pdbe.org/1ez1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ez1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ez1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ez1 ProSAT]</span></td></tr>
-Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase., Thoden JB, Firestine S, Nixon A, Benkovic SJ, Holden HM, Biochemistry. 2000 Aug 1;39(30):8791-802. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10913290 10913290]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PURT_ECOLI PURT_ECOLI] Catalyzes two reactions: the first one is the production of beta-formyl glycinamide ribonucleotide (GAR) from formate, ATP and beta GAR; the second, a side reaction, is the production of acetyl phosphate and ADP from acetate and ATP.[HAMAP-Rule:MF_01643]
+== 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/ez/1ez1_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=1ez1 ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Benkovic, S.J.]]
+[[Category: Benkovic SJ]]
-[[Category: Firestine, S.]]
+[[Category: Firestine S]]
-[[Category: Holden, H.M.]]
+[[Category: Holden HM]]
-[[Category: Nixon, A.]]
+[[Category: Nixon A]]
-[[Category: Thoden, J.B.]]
+[[Category: Thoden JB]]
-[[Category: ACT]]
-[[Category: ANP]]
-[[Category: GAR]]
-[[Category: MG]]
-[[Category: MPO]]
-[[Category: NA]]
-[[Category: atp-grasp]]
-[[Category: purine biosynthesis]]
-[[Category: transformylase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:27:13 2007''