1f9h: Difference between revisions

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-[[Image:1f9h.png|left|200px]]
-{{STRUCTURE_1f9h|  PDB=1f9h  |  SCENE=  }}
+==CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF E. COLI HPPK(R92A) WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 1.50 ANGSTROM RESOLUTION==
+<StructureSection load='1f9h' size='340' side='right'caption='[[1f9h]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1f9h]] is a 1 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=1F9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F9H 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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</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=1f9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f9h OCA], [https://pdbe.org/1f9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f9h RCSB], [https://www.ebi.ac.uk/pdbsum/1f9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f9h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HPPK_ECOLI HPPK_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/f9/1f9h_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=1f9h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate biosynthetic pathway. Arginine residues 82 and 92, strictly conserved in 35 HPPK sequences, play dynamic roles in the catalytic cycle of the enzyme. At 0.89-A resolution, two distinct conformations are observed for each of the two residues in the crystal structure of the wild-type HPPK in complex with two HP variants, two Mg(2+) ions, and an ATP analogue. Structural information suggests that R92 first binds to the alpha-phosphate group of ATP and then shifts to interact with the beta-phosphate as R82, which initially does not bind to ATP, moves in and binds to alpha-phosphate when the pyrophosphoryl transfer is about to occur. The dynamic roles of R82 and R92 are further elucidated by five more crystal structures of two mutant proteins, R82A and R92A, with and without bound ligands. Two oxidized forms of HP are observed with an occupancy ratio of 0.50:0.50 in the 0.89-A structure. The oxidation of HP has significant impact on its binding to the protein as well as the conformation of nearby residue W89.
-===CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF E. COLI HPPK(R92A) WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 1.50 ANGSTROM RESOLUTION===
+Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: crystallographic studies.,Blaszczyk J, Li Y, Shi G, Yan H, Ji X Biochemistry. 2003 Feb 18;42(6):1573-80. PMID:12578370<ref>PMID:12578370</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1f9h" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[1f9h]] is a 1 chain structure with 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=1F9H OCA].
+*[[HPPK 3D structures|HPPK 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:012578370</ref><references group="xtra"/>
+__TOC__
-[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Blaszczyk, J.]]
+[[Category: Large Structures]]
-[[Category: Ji, X.]]
+[[Category: Blaszczyk J]]
-[[Category: 6-hydroxymethyl-7]]
+[[Category: Ji X]]
-[[Category: 8-dihydropterin]]
-[[Category: Antimicrobial agent]]
-[[Category: Catalytic mechanism]]
-[[Category: Drug design]]
-[[Category: Folate]]
-[[Category: Hppk]]
-[[Category: Pterin]]
-[[Category: Pyrophosphokinase]]
-[[Category: Pyrophosphoryl transfer]]
-[[Category: Substrate specificity]]
-[[Category: Ternary complex]]
-[[Category: Transferase]]