1q0n: Difference between revisions

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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 with , , , and as ligands. This structure supersedes the now removed PDB entry 1EQO. Active as 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase, with EC number 2.7.6.3 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

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-[[Image:1q0n.gif|left|200px]]<br /><applet load="1q0n" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1q0n.gif|left|200px]]<br /><applet load="1q0n" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1q0n, resolution 1.25&Aring;" />
 '''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'''<br />
 ==Overview==
-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.
+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 Structure==
-Q0N 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, CL, ACT, APC and PH2 as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1EQO. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Q0N OCA].
+Q0N 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 <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=ACT:'>ACT</scene>, <scene name='pdbligand=APC:'>APC</scene> and <scene name='pdbligand=PH2:'>PH2</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1EQO. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0N OCA].
 ==Reference==
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 [[Category: x-ray crystallography]]
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