1q0n: Difference between revisions

Revision as of 05:43, 3 May 2008

CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE FROM E. COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 1.25 ANGSTROM RESOLUTION

OverviewOverview

BACKGROUND: Folates are essential for life. Unlike mammals, most microorganisms must synthesize folates de novo. 6-Hydroxymethyl-7, 8-dihydropterin pyrophosphokinase (HPPK) catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate pathway, and therefore is an ideal target for developing novel antimicrobial agents. HPPK from Escherichia coli is a 158-residue thermostable protein that provides a convenient model system for mechanistic studies. Crystal structures have been reported for HPPK without bound ligand, containing an HP analog, and complexed with an HP analog, two Mg(2+) ions, and ATP. RESULTS: We present the 1.25 A crystal structure of HPPK in complex with HP, two Mg(2+) ions, and AMPCPP (an ATP analog that inhibits the enzymatic reaction). This structure demonstrates that the enzyme seals the active center where the reaction occurs. The comparison with unligated HPPK reveals dramatic conformational changes of three flexible loops and many sidechains. The coordination of Mg(2+) ions has been defined and the roles of 26 residues have been derived. CONCLUSIONS: HPPK-HP-MgAMPCPP mimics most closely the natural ternary complex of HPPK and provides details of protein-substrate interactions. The coordination of the two Mg(2+) ions helps create the correct geometry for the one-step reaction of pyrophosphoryl transfer, for which we suggest an in-line single displacement mechanism with some associative character in the transition state. The rigidity of the adenine-binding pocket and hydrogen bonds are responsible for adenosine specificity. The nonconserved residues that interact with the substrate might be responsible for the species-dependent properties of an isozyme.

About this StructureAbout this Structure

1Q0N is a Single protein structure of sequence from Escherichia coli. This structure supersedes the now removed PDB entry 1eqo. Full crystallographic information is available from OCA.

ReferenceReference

Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution., Blaszczyk J, Shi G, Yan H, Ji X, Structure. 2000 Oct 15;8(10):1049-58. PMID:11080626 Page seeded by OCA on Sat May 3 05:43:18 2008

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OCA

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 [[Image:1q0n.gif|left|200px]]
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+The line below this paragraph, containing "STRUCTURE_1q0n", creates the "Structure Box" on the page.
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-|LIGAND= <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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</scene>
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-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span>
+{{STRUCTURE_1q0n|  PDB=1q0n  |  SCENE=  }}
-|GENE= FOLK OR B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
-|DOMAIN=
-|RELATEDENTRY=[[1hka|1hka]], [[1eqm|1eqm]], [[1eq0|1eq0]], [[1eqo|1eqo]], [[1ex8|1ex8]], [[1cbk|1cbk]], [[1dy3|1dy3]], [[1f9y|1f9y]], [[1f9h|1f9h]], [[1g4c|1g4c]], [[1hq2|1hq2]], [[1im6|1im6]], [[1kbr|1kbr]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0n OCA], [http://www.ebi.ac.uk/pdbsum/1q0n PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q0n RCSB]</span>
-}}
-<!-- STRUCTURE TEMPLATE END -->
 '''CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE FROM E. COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 1.25 ANGSTROM RESOLUTION'''
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 [[Category: Ternary complex]]
 [[Category: X-ray crystallography]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 05:43:18 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Apr  7 18:28:34 2008''