PDBsum entry: 2dsk

Hydrolase

PDB id: 2dsk

Contents

Protein chains

300 a.a. *

Ligands

GOL ×6

SO4

Waters ×650

* Residue conservation analysis

PDB id:

2dsk

Name:

Hydrolase

Title:

Crystal structure of catalytic domain of hyperthermophilic c from pyrococcus furiosus

Structure:

Chitinase. Chain: a, b. Fragment: catalutic domain (ad2). Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.50Å R-factor: 0.168 R-free: 0.180

Authors:

T.Nakamura,S.Mine,Y.Hagihara,K.Ishikawa,K.Uegaki

Key ref:

T.Nakamura et al. (2007). Structure of the catalytic domain of the hyperthermophilic chitinase from Pyrococcus furiosus. Acta Crystallograph Sect F Struct Biol Cryst Commun, 63, 7. PubMed id: 17183162 Ref: Full text

Date:

30-Jun-06 Release date: 06-Feb-07

Protein chains

Q8U1H5  (Q8U1H5_PYRFU) -  Putative chitinase

Seq: 717 a.a.

Struc: 300 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: catalytic activity (2 terms)

Full text	Acta Crystallograph Sect F Struct Biol Cryst Commun 63:7 (2007)
PubMed id: 17183162

Structure of the catalytic domain of the hyperthermophilic chitinase from Pyrococcus furiosus.

T.Nakamura, S.Mine, Y.Hagihara, K.Ishikawa, K.Uegaki.

ABSTRACT

The crystal structure of the catalytic domain of a chitinase from the hyperthermophilic archaeon Pyrococcus furiosus (AD2(PF-ChiA)) has been determined at 1.5 A resolution. This is the first structure of the catalytic domain of an archaeal chitinase. The overall structure of AD2(PF-ChiA) is a TIM-barrel fold with a tunnel-like active site that is a common feature of family 18 chitinases. Although the catalytic residues (Asp522, Asp524 and Glu526) are conserved, comparison of the conserved residues and structures with those of other homologous chitinases indicates that the catalytic mechanism of PF-ChiA is different from that of family 18 chitinases.

Selected figure(s)

Figure 4.
Stereoview of the overlaid structure of AD2[PF-ChiA] (grey) and the complex of chitinase B with (GlcNAc)[6] (magenta). The porch loop and the [alpha]/[beta] domain of chitinase B are shown in blue and green, respectively, and GlcNAc is shown in ball-and-stick representation. The [beta]-strands in TIM-barrel fold were used for the superposition (the r.m.s. deviation is 1.26 A between backbone atoms for 46 residues). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 January 1; 63(Pt 1): 7–11. Published online 2006 December 16. doi: 10.1107/S1744309106051773. Copyright [copyright] International Union of Crystallography 2007

Figure 7.
The conformation around Tyr590. The electron density shows a [sigma][A]-weighted F [o] [minus sign] F [c] map at the 3.0[sigma] level when three amino-acid residues (Tyr589, Tyr590 and Trp591) were removed from the structure-factor calculation. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 January 1; 63(Pt 1): 7–11. Published online 2006 December 16. doi: 10.1107/S1744309106051773. Copyright [copyright] International Union of Crystallography 2007

The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallograph Sect F Struct Biol Cryst Commun (2007, 63, 7-0) copyright 2007.

Figures were selected by an automated process.