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.


2dcf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2dcf.jpg|left|200px]]
+
{{Seed}}
 +
[[Image:2dcf.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_2dcf| PDB=2dcf | SCENE= }}
{{STRUCTURE_2dcf| PDB=2dcf | SCENE= }}
-
'''Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N mutant with substrate'''
+
===Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N mutant with substrate===
-
==Overview==
+
<!--
-
We performed X-ray crystallographic analyses of 6-aminohexanoate-dimer hydrolase (Hyb-24DN), an enzyme responsible for the degradation of nylon-6, an industry by-product, and of a complex between Hyb-24DN-A(112) (S112A-mutant of Hyb-24DN) and 6-aminohexanoate-linear dimer (Ald) at 1.58 A and 1.4 A resolution, respectively. In Hyb-24DN, Asp181-O(delta) forms hydrogen bonds with Tyr170-O(eta), -two of the catalytic and binding amino acids, and a loop between Asn167 and Val177. This state is the so-called open form, allowing its substrate to bind in the space between the loop and catalytic residues. Upon substrate binding (in Hyb-24DN-A(112)/Ald complex), the loop is shifted 4.3 A at Tyr170-C(alpha), and the side-chain of Tyr170 is rotated. By the combined effect, Tyr170-O(eta) moves a total of 10.5 A, resulting in the formation of hydrogen bonds with the nitrogen of amide linkage in Ald (closed form). In addition, electrostatic interaction between Asp181-O(delta) and the amino group in Ald stabilizes the substrate binding. We propose here that the enzyme catalysis proceeds according to the following steps: (i) Ald-induced transition from open to closed form, (ii) nucleophilic attack of Ser112 to Ald and formation of a tetrahedral intermediate, (iii) formation of acyl enzyme and transition to open form, (iv) deacylation. Amino acid substitutions reducing the enzyme/Ald interaction at positions 181 or 170 drastically decreased the Ald-hydrolytic activity, but had very little effect on esterolytic activity, suggesting that esterolytic reaction proceeds regardless of conversion. Present models illustrate why new activity against the nylon oligomer has evolved in an esterase with beta-lactamase folds, while retaining the original esterolytic functions.
+
The line below this paragraph, {{ABSTRACT_PUBMED_17512009}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 17512009 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_17512009}}
==About this Structure==
==About this Structure==
Line 29: Line 33:
[[Category: Takeo, M.]]
[[Category: Takeo, M.]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 28 09:28:06 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 12:43:48 2008''

Revision as of 09:43, 28 July 2008

Image:2dcf.png

Template:STRUCTURE 2dcf

Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N mutant with substrate

Template:ABSTRACT PUBMED 17512009

About this Structure

2DCF is a Single protein structure of sequence from Flavobacterium sp.. Full crystallographic information is available from OCA.

Reference

Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase., Negoro S, Ohki T, Shibata N, Sasa K, Hayashi H, Nakano H, Yasuhira K, Kato D, Takeo M, Higuchi Y, J Mol Biol. 2007 Jun 29;370(1):142-56. Epub 2007 Apr 24. PMID:17512009

Page seeded by OCA on Mon Jul 28 12:43:48 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

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