PDBsum entry: 1gpi

Hydrolase

PDB-id: 1gpi

Biological unit = asymmetric unit, as shown
(as defined in PDB file)

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PROCHECK

Protein chain

431 a.a. *

Ligands

NAG

Waters ×447

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1gpi

Name:

Hydrolase

Title:

Cellobiohydrolase cel7d (cbh 58) from phanerochaete chrysosporium. Catalytic module at 1.32 ang resolution

Structure:

Exoglucanase i. Chain: a. Fragment: catalytic module, residues 19-449. Synonym: 1,4-beta-d-glucan cellobiohydrolase cel7d, exocellobiohydrolase i, cellobiohydrolase i, cbh58, cbh1, cbh i, cbh1.2. Other_details: link NAG-asn (NAG 435 and nd2 asn 286) cispep tyr 378, cispep pro 379, ssbond 1 cys 19 cys 25, ssbond 2 cys 50 cys 71

Source:

Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: k3. Atcc: 32629. Other_details: extracellular protein obtained from the fed-batch cultivation of p. Chrysosporium strain k3 using cellulose (avicel) as a carbon source

Biological unit:

Monomer (from PDB file)

UniProt:

Q09431 (Q09431_PHACH)

Seq:

Struc:

Seq:

511 a.a.

Struc:

431 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme class:

E.C.3.2.1.91   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Hydrolysis of 1,4-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains.

Resolution:

1.32Å

R-factor:

0.216

R-free:

0.242

Authors:

I.G.Munoz,S.L.Mowbray,J.Stahlberg

Key ref:

I.G.Muñoz et al. (2001). Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 A resolution and homology models of the isozymes.. J Mol Biol, 314, 1097-1111. [PubMed id: 11743726] [DOI: 10.1006/jmbi.2000.5180]

Date:

05-Nov-01

Release date:

01-Jan-02

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Key reference

DOI no: 10.1006/jmbi.2000.5180

J Mol Biol 314:1097-1111 (2001)

PubMed id: 11743726

Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 A resolution and homology models of the isozymes.

I.G.Muñoz, W.Ubhayasekera, H.Henriksson, I.Szabó, G.Pettersson, G.Johansson, S.L.Mowbray, J.Ståhlberg.

ABSTRACT

Cellobiohydrolase 58 (Cel7D) is the major cellulase produced by the white-rot fungus Phanerochaete chrysosporium, constituting approximately 10 % of the total secreted protein in liquid culture on cellulose. The enzyme is classified into family 7 of the glycosyl hydrolases, together with cellobiohydrolase I (Cel7A) and endoglucanase I (Cel7B) from Trichoderma reesei. Like those enzymes, it catalyses cellulose hydrolysis with net retention of the anomeric carbon configuration.The structure of the catalytic module (431 residues) of Cel7D was determined at 3.0 A resolution using the structure of Cel7A from T. reesei as a search model in molecular replacement, and ultimately refined at 1.32 A resolution. The core structure is a beta-sandwich composed of two large and mainly antiparallel beta-sheets packed onto each other. A long cellulose-binding groove is formed by loops on one face of the sandwich. The catalytic residues are conserved and the mechanism is expected to be the same as for other family members. The Phanerochaete Cel7D binding site is more open than that of the T. reesei cellobiohydrolase, as a result of deletions and other changes in the loop regions, which may explain observed differences in catalytic properties. The binding site is not, however, as open as the groove of the corresponding endoglucanase. A tyrosine residue at the entrance of the tunnel may be part of an additional subsite not present in the T. reesei cellobiohydrolase.The Cel7D structure was used to model the products of the five other family 7 genes found in P. chrysosporium. The results suggest that at least two of these will have differences in specificity and possibly catalytic mechanism, thus offering some explanation for the presence of Cel7 isozymes in this species, which are differentially expressed in response to various growth conditions.

Selected figure(s)

Figure 1.
Figure 1. Structure of the Pc_Cel7D catalytic module. In a ribbon drawing of the enzyme, b- sheets are shown in purple, helical segments in blue, and loop regions in cyan. Ball-and-stick represen- tations of the catalytic residues are coloured red, while residues of the substrate-binding tunnel are green (tryptophan or tyrosine) or yellow (arginine). The N-acetyl glucosa- mine is shown in pink. Figures 1 and 2 were prepared using MolScript 68 and POV-Ray (http:// www.povray.org).

Figure 2.
Figure 2. Comparison of Pc_Cel7D with Tr_Cel7A. Pc_Cel7D is coloured in cyan and Tr_Cel7A in yellow. (a) The backbone of Tr_Cel7A with a modelled cellulose chain (RCSB Protein Data Bank entry code 8CEL) is superimposed on that of Pc_Cel7D, in a divergent stereo view. The cellulose chain is shown using a ball-and-stick representation in atomic colours. The catalytic carboxylate residues are coloured pink. Three deletions in Pc_Cel7D with respect to Tr_Cel7A are indicted by red broken circles, and are shown in more detail in (b), (c) and (d). (b) A deletion near site -6 makes the entrance to the cellulose-binding the tunnel more open in Pc_Cel7D. Trp40 is conserved in both enzymes at subsite -7, but an extra aromatic residue in Pc_Cel7D may bind an additional glucosyl residue in a potential -8 site. (c) In Pc_Cel7D, a deletion at the tip of one loop, together with smaller side-chains in the opposing loop, will combine to make the substrate more exposed at the -4 and -3 sites. (d) Deletion in a loop found in Tr_Cel7A, and replacement of Tyr371 with Ala368, make the catalytic site more exposed in Pc_Cel7D.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 1097-1111) copyright 2001.

Figures were selected by an automated process.