This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2kzz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2kzz.gif|left|200px]]
+
{{Seed}}
 +
[[Image:2kzz.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_2kzz| PDB=2kzz | SCENE= }}
{{STRUCTURE_2kzz| PDB=2kzz | SCENE= }}
-
'''KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY'''
+
===KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY===
-
==Overview==
+
<!--
-
The interaction of a divalent metal ion with a leaving 3' oxygen is a central component of several proposed mechanisms of phosphoryl transfer. In support of this are recent kinetic studies showing that thiophilic metal ions (e.g., Mn2+) stimulate the hydrolysis of compounds in which sulfur takes the place of the leaving oxygen. To examine the structural basis of this phenomenon, we have solved four crystal structures of single-stranded DNA's containing either oxygen or sulfur at a 3'-bridging position bound in conjunction with various metal ions at the 3'-5' exonucleolytic active site of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli. Two structures of normal ssDNA bound to KF in the presence of Zn2+ and Mn2+ or Zn2+ alone were refined at 2.6- and 2.25-A resolution, respectively. They serve as standards for comparison with other Mn2+- and Zn2+-containing structures. In these cases, Mn2+ and Zn2+ bind at metal ion site B in a nearly identical position to Mg2+ (Brautigam and Steitz (1998) J. Mol. Biol. 277, 363-377). Two structures of KF bound to a deoxyoligonucleotide that contained a 3'-bridging sulfur at the scissile phosphate were refined at 2.03-A resolution. Although the bridging sulfur compounds bind in a manner very similar to that of the normal oligonucleotides, the presence of the sulfur changes the metal ion binding properties of the active site such that Mn2+ and Zn2+ are observed at metal ion site B, but Mg2+ is not. It therefore appears that the ability of the bridging sulfur compounds to exclude nonthiophilic metal ions from metal ion site B explains the low activity of KF exonuclease on these substrates in the presence of Mg2+ (Curley et al. (1997) J. Am. Chem. Soc. 119, 12691-12692) and that the 3'-bridging atom of the substrate is influencing the binding of metal ion B prior to catalysis.
+
The line below this paragraph, {{ABSTRACT_PUBMED_9888810}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 9888810 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_9888810}}
==About this Structure==
==About this Structure==
Line 31: Line 35:
[[Category: Polymerase]]
[[Category: Polymerase]]
[[Category: Two metal ion]]
[[Category: Two metal ion]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 09:29:32 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 19:04:31 2008''

Revision as of 16:04, 27 July 2008

Image:2kzz.png

Template:STRUCTURE 2kzz

KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY

Template:ABSTRACT PUBMED 9888810

About this Structure

2KZZ is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli., Brautigam CA, Sun S, Piccirilli JA, Steitz TA, Biochemistry. 1999 Jan 12;38(2):696-704. PMID:9888810

Page seeded by OCA on Sun Jul 27 19:04:31 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2kzz"
Personal tools