1eqm: Difference between revisions

Revision as of 15:24, 2 May 2008

CRYSTAL STRUCTURE OF BINARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE WITH ADENOSINE-5'-DIPHOSPHATE

OverviewOverview

The crystal structure of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in complex with MgADP has been determined at 1.5-A resolution with a crystallographic R factor of 0.191. The solution structure of HPPK in complex with Mg(2+) and beta,gamma-methyleneadenosine 5'-triphosphate (MgAMPPCP) has been determined using a simulated annealing protocol with 3,523 experimental NMR restraints. The root mean square deviation of the ensemble of 20 refined conformers that represent the solution structure from the mean coordinate set derived from them is 0.74 +/- 0.26 A for all backbone atoms and 0.49 +/- 0.22 A when residues Pro(14), Pro(44)-Gln(50), and Arg(84)-Pro(91) are excluded. Binding of MgADP causes significant changes in the conformation and dynamical property of three loops of HPPK that are involved in catalysis. A dramatic, unusual conformational change is that loop 3 moves away from the active center significantly with some residues moving by >17 A. The binding of MgADP also stabilizes loop 1 and loop 3 but makes loop 2 more mobile. Very similar conformational and dynamical changes are observed in the NMR solution structure of HPPK.MgAMPPCP. The conformational and dynamical changes may play important roles in both substrate binding and product release in the catalytic cycle.

About this StructureAbout this Structure

1EQM is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR., Xiao B, Shi G, Gao J, Blaszczyk J, Liu Q, Ji X, Yan H, J Biol Chem. 2001 Oct 26;276(43):40274-81. Epub 2001 Aug 23. PMID:11546767 Page seeded by OCA on Fri May 2 15:24:46 2008

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OCA

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 [[Image:1eqm.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1eqm |SIZE=350|CAPTION= <scene name='initialview01'>1eqm</scene>, resolution 1.50&Aring;
+The line below this paragraph, containing "STRUCTURE_1eqm", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|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>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1eqm|  PDB=1eqm  |  SCENE=  }}
-|RELATEDENTRY=[[1eq0|1EQ0]], [[1eqo|1EQO]], [[1hka|1HKA]], [[1cbk|1CBK]], [[1dy3|1DY3]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1eqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eqm OCA], [http://www.ebi.ac.uk/pdbsum/1eqm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1eqm RCSB]</span>
-}}
 '''CRYSTAL STRUCTURE OF BINARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE WITH ADENOSINE-5'-DIPHOSPHATE'''
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 [[Category: Ji, X.]]
 [[Category: Xiao, B.]]
-[[Category: antimicrobial agent]]
+[[Category: Antimicrobial agent]]
-[[Category: drug design]]
+[[Category: Drug design]]
-[[Category: folate]]
+[[Category: Folate]]
-[[Category: hppk]]
+[[Category: Hppk]]
-[[Category: pterin]]
+[[Category: Pterin]]
-[[Category: pyrophosphokinase]]
+[[Category: Pyrophosphokinase]]
-[[Category: pyrophosphoryl transfer]]
+[[Category: Pyrophosphoryl transfer]]
-[[Category: substrate specificity]]
+[[Category: Substrate specificity]]
-[[Category: x-ray crystallography]]
+[[Category: X-ray crystallography]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 15:24:46 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:07:51 2008''