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.


2ia5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2ia5.gif|left|200px]]
+
{{Seed}}
 +
[[Image:2ia5.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_2ia5| PDB=2ia5 | SCENE= }}
{{STRUCTURE_2ia5| PDB=2ia5 | SCENE= }}
-
'''T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium.'''
+
===T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium.===
-
==Overview==
+
<!--
-
T4 polynucleotide kinase/phosphatase (Pnkp) exemplifies a family of bifunctional enzymes with 5'-kinase and 3' phosphatase activities that function in nucleic acid repair. T4 Pnkp is a homotetramer of a 301-aa polypeptide, which consists of an N-terminal kinase domain of the P-loop phosphotransferase superfamily and a C-terminal phosphatase domain of the DxD acylphosphatase superfamily. The homotetramer is formed via pairs of phosphatase-phosphatase and kinase-kinase homodimer interfaces. Here we identify four side chains-Asp187, Ser211, Lys258, and Asp277-that are required for 3' phosphatase activity. Alanine mutations at these positions abolished phosphatase activity without affecting kinase function or tetramerization. Conservative substitutions of asparagine or glutamate for Asp187 did not revive the 3' phosphatase, nor did arginine or glutamine substitutions for Lys258. Threonine in lieu of Ser211 and glutamate in lieu of Asp277 restored full activity, whereas asparagine at position 277 had no salutary effect. We report a 3.0 A crystal structure of the Pnkp tetramer, in which a sulfate ion is coordinated between Arg246 and Arg279 in a position that we propose mimics one of the penultimate phosphodiesters (5'NpNpNp-3') of the polynucleotide 3'-PO(4) substrate. The amalgam of mutational and structural data engenders a plausible catalytic mechanism for the phosphatase that includes covalent catalysis (via Asp165), general acid-base catalysis (via Asp167), metal coordination (by Asp165, Asp277 and Asp278), and transition state stabilization (via Lys258, Ser211, backbone amides, and the divalent cation). Other critical side chains play architectural roles (Arg176, Asp187, Arg213, Asp254). To probe the role of oligomerization in phosphatase function, we introduced six double-alanine cluster mutations at the phosphatase-phosphatase domain interface, two of which (R297A-Q295A and E292A-D300A) converted Pnkp from a tetramer to a dimer and ablated phosphatase activity.
+
The line below this paragraph, {{ABSTRACT_PUBMED_17493655}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 17493655 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_17493655}}
==About this Structure==
==About this Structure==
Line 29: Line 33:
[[Category: Zhu, H.]]
[[Category: Zhu, H.]]
[[Category: Polynucleotide kinase phosphatase sulfate-complex]]
[[Category: Polynucleotide kinase phosphatase sulfate-complex]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 07:14:56 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:22:18 2008''

Revision as of 06:22, 29 July 2008

Image:2ia5.png

Template:STRUCTURE 2ia5

T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium.

Template:ABSTRACT PUBMED 17493655

About this Structure

2IA5 is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.

Reference

Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase., Zhu H, Smith P, Wang LK, Shuman S, Virology. 2007 Sep 15;366(1):126-36. Epub 2007 May 9. PMID:17493655

Page seeded by OCA on Tue Jul 29 09:22:18 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ia5"
Personal tools