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.


1eni

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1eni.jpg|left|200px]]
+
{{Seed}}
 +
[[Image:1eni.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_1eni| PDB=1eni | SCENE= }}
{{STRUCTURE_1eni| PDB=1eni | SCENE= }}
-
'''CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS'''
+
===CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS===
-
==Overview==
+
<!--
-
Crystallographic study of bacteriophage T4 endonuclease V, which is involved in the initial step of the pyrimidine dimer-specific excision repair pathway, has been carried out with respect to the wild-type and three different mutant enzymes. This enzyme catalyzes the cleavage of the N-glycosyl bond at the 5'-side of the pyrimidine dimer, and subsequently incises the phosphodiester bond at the apyrimidinic site through a beta-elimination reaction. The structure of the wild-type enzyme refined at 1.45 A resolution reveals the detailed molecular architecture. The enzyme is composed of a single compact domain classified as an all-alpha structure. The molecule is stabilized mainly by three hydrophobic cores, two of which include many aromatic side-chain interactions. The structure has a unique folding motif, where the amino-terminal segment penetrates between two major alpha-helices and prevents their direct contact, and it is incompatible with the close-packing category of helices for protein folding. The concave surface, covered with many positive charges, implies an interface for DNA binding. The glycosylase catalytic center, which comprises Glu23 and the surrounding basic residues Arg3, Arg22 and Arg26, lie in this basic surface. The crystal structures of the three active-site mutants, in which Glu23 was replaced by Gln(E23Q) and Asp (E23D), respectively, and Arg3 by Gln (R3Q), have been determined at atomic resolution. The backbone structures of the E23Q and R3Q mutants were almost identical with that of the wild-type, while the E23D mutation induces a small, but significant, change in the backbone structure, such as an increase of the central kink of the H1 helix at Pro25. In the catalytic center of the glycosylase, however, these three mutations do not generate notable movements of protein atoms, except for significant shifts of some bound water molecules. Thus, the structural differences between the wild-type and each mutant are confined to the remarkably small region around their replaced chemical groups. Combined with the biochemical studies and the difference circular dichroism measurements, these results allow us to conclude that the negatively charged carboxyl group of Glu23 is essential for the cleavage of the N-glycosyl bond, and that the positively charged guanidino group of Arg3 is crucial to bind the substrate, a DNA duplex containing a pyrimidine dimer. The amino terminal alpha-amino group is located at a position approximately 4.4 A away from the carboxyl group of Glu23. These structural features are generally consistent with the reaction scheme proposed by Dodson and co-workers.
+
The line below this paragraph, {{ABSTRACT_PUBMED_7783199}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 7783199 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_7783199}}
==About this Structure==
==About this Structure==
Line 29: Line 33:
[[Category: Vassylyev, D G.]]
[[Category: Vassylyev, D G.]]
[[Category: Endonuclease]]
[[Category: Endonuclease]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:18:47 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 01:05:40 2008''

Revision as of 22:05, 30 June 2008

Image:1eni.png

Template:STRUCTURE 1eni

CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS

Template:ABSTRACT PUBMED 7783199

About this Structure

1ENI is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.

Reference

Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants., Morikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E, J Mol Biol. 1995 Jun 2;249(2):360-75. PMID:7783199

Page seeded by OCA on Tue Jul 1 01:05:40 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1eni"
Personal tools