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==Crystal structure of E. coli HPPK in complex with MgAMPCPP and 6-hydroxymethylpterin/6-carboxypterin== | ==Crystal structure of E. coli HPPK in complex with MgAMPCPP and 6-hydroxymethylpterin/6-carboxypterin== | ||
<StructureSection load='3ip0' size='340' side='right' caption='[[3ip0]], [[Resolution|resolution]] 0.89Å' scene=''> | <StructureSection load='3ip0' size='340' side='right'caption='[[3ip0]], [[Resolution|resolution]] 0.89Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ip0]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3ip0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3h4a 3h4a] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1f9y 1f9y]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IP0 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=HHS:6-CARBOXYPTERIN'>HHS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | </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=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=HHS:6-CARBOXYPTERIN'>HHS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1q0n|1q0n]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q0n|1q0n]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ip0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ip0 OCA], [https://pdbe.org/3ip0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ip0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ip0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ip0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
| Line 14: | Line 14: | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/3ip0_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/3ip0_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 29: | Line 29: | ||
</div> | </div> | ||
<div class="pdbe-citations 3ip0" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3ip0" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[HPPK 3D structures|HPPK 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 35: | Line 38: | ||
[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]] | [[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]] | ||
[[Category: Ecoli]] | [[Category: Ecoli]] | ||
[[Category: Large Structures]] | |||
[[Category: Blaszczyk, J]] | [[Category: Blaszczyk, J]] | ||
[[Category: Ji, X]] | [[Category: Ji, X]] | ||
Revision as of 06:37, 21 April 2022
Crystal structure of E. coli HPPK in complex with MgAMPCPP and 6-hydroxymethylpterin/6-carboxypterinCrystal structure of E. coli HPPK in complex with MgAMPCPP and 6-hydroxymethylpterin/6-carboxypterin
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed6-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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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