PDBsum entry: 1ks8

Hydrolase

PDB-id: 1ks8

Asymmetric unit

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PROCHECK

Protein chain

433 a.a. *

Ligands

SO4

Waters ×729

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, dimer
(*as deduced by PQS)

PDB id:

1ks8

Name:

Hydrolase

Title:

The structure of endoglucanase from termite, nasutitermes takasagoensis, at ph 2.5.

Structure:

Endo-b-1,4-glucanase. Chain: a. Fragment: catalytic domain. Engineered: yes

Source:

Nasutitermes takasagoensis. Organism_taxid: 62960. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biological unit:

Dimer (from PQS)

UniProt:

O77044 (O77044_9NEOP)

Seq:

Struc:

Seq:

448 a.a.

Struc:

433 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme class:

E.C.3.2.1.4   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.

Resolution:

1.40Å

R-factor:

0.177

R-free:

0.191

Authors:

S.Khademi,L.A.Guarino,H.Watanabe,G.Tokuda,E.F.Meyer

Key ref:

S.Khademi et al. (2002). Structure of an endoglucanase from termite, Nasutitermes takasagoensis.. Acta Crystallogr D Biol Crystallogr, 58, 653-659. [PubMed id: 11914490] [DOI: 10.1107/S0907444902002366]

Date:

11-Jan-02

Release date:

21-Jan-03

Related entries:

1ksc
1ksd

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Clefts

Surface

Key reference

DOI no: 10.1107/S0907444902002366

Acta Crystallogr D Biol Crystallogr 58:653-659 (2002)

PubMed id: 11914490

Structure of an endoglucanase from termite, Nasutitermes takasagoensis.

S.Khademi, L.A.Guarino, H.Watanabe, G.Tokuda, E.F.Meyer.

ABSTRACT

Contrary to conventional wisdom, it has been shown recently that termites do not necessarily depend on symbiotic bacteria to process cellulose. They secrete their own cellulases, mainly endo-beta-1,4-glucanase and beta-1,4-glucosidase. Here, the first structure of an endogenous endoglucanase from the higher termite Nasutitermes takasagoensis (NtEgl) is reported at 1.40 A resolution. NtEgl has the general folding of an (alpha/alpha)(6) barrel, which is a common folding pattern for glycosyl hydrolase family 9. Three-dimensional structural analysis shows that the conserved Glu412 is the catalytic acid/base residue and the conserved Asp54 or Asp57 is the base. The enzyme has a Ca(2+)-binding site near its substrate-binding cleft. Comparison between the structure of the Ca(2+)-free enzyme produced by reducing the pH of the soaked crystal from 5.6 (the pH of optimum enzyme activity) to 2.5 with that of the Ca(2+)-bound enzyme did not show significant differences in the locations of the C(alpha) atoms. The main differences are in the conformation of the residue side chains ligating the Ca(2+) ion. The overall structure of NtEgl at pH 6.5 is similar to that at pH 5.6. The major change observed was in the conformation of the side chain of the catalytic acid/base Glu412, which rotates from a hydrophobic cavity to a relatively hydrophilic environment. This side-chain displacement may decrease the enzyme activity at higher pH.

Selected figure(s)

Figure 2.
Figure 2 The structure of NtEgl. (a) Ribbon representation of NtEgl showing top view of 12 helices. Outer helices are in green, inner helices are red, -strands are blue and the Ca^2+ ion is brown. (b) Surface potential of NtEgl showing the binding cleft. The ribbon representation of NtEgl is visible through the transparent molecular surface, with positive charges in blue and negative charges in red; the Ca^2+ ion is green.

Figure 5.
Figure 5 The superposition of residues Asp54, Asp57 and Glu412 from NtEgl (in blue) on 55, 58 and 424 from CelD (in green) and 198, 201 and 555 from E4 (in red), respectively.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 653-659) copyright 2002.

Figures were selected by an automated process.