1kfd: Difference between revisions

Revision as of 22:40, 2 May 2008

CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE

OverviewOverview

Crystal structures of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli complexed with deoxynucleoside triphosphate (dNTP) or with pyrophosphate (PPi) determined to 3.9-A resolution by X-ray crystallography show these molecules binding within the cleft of the polymerase domain and surrounded by residues previously implicated in dNTP binding. The dNTP binds adjacent to the O-helix [Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., & Steitz, T. A. (1985a) Nature 313, 762-766] with its triphosphate moiety anchored by three positively charged residues, Arg 754, Arg 682, and Lys 758, plus His 734 and Gln 708. The dNTP binding site observed in the crystal is consistent with the results of chemical modification including cross-linking and is also near many of the amino acid residues whose mutation affects catalysis [Polesky, A. H., Steitz, T. A., Grindley, N. D. F., & Joyce, C. M. (1990) J. Biol. Chem. 265, 14579-14591; Polesky, A. H., Dahlberg, M. E., Benkovic, S. J., Grindley, N. D. F., & Joyce, C. M. (1992) J. Biol. Chem. 267, 8417-8428]. However, we conclude that the position of at least the dNMP moiety of dNTP in the binary complex is not likely to be the same as in its catalytically relevant complex with primer-template DNA.

About this StructureAbout this Structure

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

ReferenceReference

Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate., Beese LS, Friedman JM, Steitz TA, Biochemistry. 1993 Dec 28;32(51):14095-101. PMID:8260491 Page seeded by OCA on Fri May 2 22:40:49 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:1kfd.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 1kfd |SIZE=350|CAPTION= <scene name='initialview01'>1kfd</scene>, resolution 3.9&Aring;
+The line below this paragraph, containing "STRUCTURE_1kfd", 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=CTP:CYTIDINE-5&#39;-TRIPHOSPHATE'>CTP</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/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1kfd|  PDB=1kfd  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kfd OCA], [http://www.ebi.ac.uk/pdbsum/1kfd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kfd RCSB]</span>
-}}
 '''CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE'''
@@ Line 29: / Line 26: @@
 [[Category: Friedman, J M.]]
 [[Category: Steitz, T A.]]
-[[Category: nucleotidyltransferase]]
+[[Category: Nucleotidyltransferase]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 22:40:49 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:47:47 2008''