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1q0n

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Revision as of 07:40, 9 December 2020

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

Structural highlights

1q0n is a 1 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. This structure supersedes the now removed PDB entry 1eqo. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Related:	1hka, 1eqm, 1eq0, 1eqo, 1ex8, 1cbk, 1dy3, 1f9y, 1f9h, 1g4c, 1hq2, 1im6, 1kbr
Gene:	FOLK OR B0142 ("Bacillus coli" Migula 1895)
Activity:	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase, with EC number 2.7.6.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Blaszczyk J, Shi G, Yan H, Ji X. Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution. Structure. 2000 Oct 15;8(10):1049-58. PMID:11080626

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1q0n"

@@ Line 1: / Line 1: @@
 ==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==
-<StructureSection load='1q0n' size='340' side='right' caption='[[1q0n]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
+<StructureSection load='1q0n' size='340' side='right'caption='[[1q0n]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1q0n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1eqo 1eqo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q0N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1q0n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1eqo 1eqo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q0N 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</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=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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[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]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[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]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FOLK OR B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1q0n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q0n RCSB], [http://www.ebi.ac.uk/pdbsum/1q0n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0n ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1q0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0n OCA], [http://pdbe.org/1q0n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q0n RCSB], [http://www.ebi.ac.uk/pdbsum/1q0n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0n ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 1q0n" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[HPPK 3D structures|HPPK 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 38: @@
 [[Category: Bacillus coli migula 1895]]
 [[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
+[[Category: Large Structures]]
 [[Category: Blaszczyk, J]]
 [[Category: Ji, X]]

1q0n

From Proteopedia

Revision as of 07:40, 9 December 2020

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

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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