PDBsum entry 2vtc

Hydrolase

PDB id: 2vtc

Contents

Protein chains

228 a.a. *

Ligands

NAG-NAG ×2

Metals

_NI ×3

Waters ×605

* Residue conservation analysis

PDB id:

2vtc

Name:

Hydrolase

Title:

The structure of a glycoside hydrolase family 61 member, cel61b from the hypocrea jecorina.

Structure:

Cel61b. Chain: a, b. Synonym: cellulase

Source:

Hypocrea jecorina. Organism_taxid: 51453. Other_details: synonym trichoderma reesei

Resolution:

1.60Å R-factor: 0.197 R-free: 0.220

Authors:

S.Karkehabadi,H.Hansson,S.Kim,K.Piens,C.Mitchinson,M.Sandgren

Key ref:

S.Karkehabadi et al. (2008). The first structure of a glycoside hydrolase family 61 member, Cel61B from Hypocrea jecorina, at 1.6 A resolution. J Mol Biol, 383, 144-154. PubMed id: 18723026 DOI: 10.1016/j.jmb.2008.08.016

Date:

14-May-08 Release date: 09-Sep-08

Protein chains

Q7Z9M7  (GUN7_HYPJQ) -  AA9 family lytic polysaccharide monooxygenase cel61B from Hypocrea jecorina (strain QM6a)

Seq: 249 a.a.

Struc: 228 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.99.56 - lytic cellulose monooxygenase (C4-dehydrogenating).
• Reaction: [(1->4)-beta-D-glucosyl]n+m + reduced acceptor + O2 = 4-dehydro-beta-D- glucosyl-[(1->4)-beta-D-glucosyl]n-1 + [(1->4)-beta-D-glucosyl]m + acceptor + H2O
• Cofactor: Cu(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1016/j.jmb.2008.08.016

J Mol Biol 383:144-154 (2008)

PubMed id: 18723026

The first structure of a glycoside hydrolase family 61 member, Cel61B from Hypocrea jecorina, at 1.6 A resolution.

S.Karkehabadi, H.Hansson, S.Kim, K.Piens, C.Mitchinson, M.Sandgren.

ABSTRACT

The glycoside hydrolase (GH) family 61 is a long-recognized, but still recondite, class of proteins, with little known about the activity, mechanism or function of its more than 70 members. The best-studied GH family 61 member, Cel61A of the filamentous fungus Hypocrea jecorina, is known to be an endoglucanase, but it is not clear if this represents the main activity or function of this family in vivo. We present here the first structure for this family, that of Cel61B from H. jecorina. The best-quality crystals were formed in the presence of nickel, and the crystal structure was solved to 1.6 A resolution using a single-wavelength anomalous dispersion method with nickel as the source of anomalous scatter. Cel61B lacks a carbohydrate-binding module and is a single-domain protein that folds into a twisted beta-sandwich. A structure-aided sequence alignment of all GH family 61 proteins identified a highly conserved group of residues on the surface of Cel61B. Within this patch of mostly polar amino acids was a site occupied by the intramolecular nickel hexacoordinately bound in the solved structure. In the Cel61B structure, there is no easily identifiable carbohydrate-binding cleft or pocket or catalytic center of the types normally seen in GHs. A structural comparison search showed that the known structure most similar to Cel61B is that of CBP21 from the Gram-negative soil bacterium Serratia marcescens, a member of the carbohydrate-binding module family 33 proteins. A polar surface patch highly conserved in that structural family has been identified in CBP21 and shown to be involved in chitin binding and in the protein's enhancement of chitinase activities. The analysis of the Cel61B structure is discussed in light of our continuing research to better understand the activities and function of GH family 61.

Selected figure(s)

Figure 2.
Fig. 2. Secondary-structure representation of the two Cel61B molecules in the asymmetric unit, colored from blue to red from the N-terminus to the C-terminus of each protein molecule. Shown in grey are the side chains of the Asn6 and the two NAG molecules, His1, His89 and Tyr176. The nickel ions and their coordinating water molecules are depicted as spheres of green and red, respectively.

Figure 3.
Fig. 3. Topology diagram of Cel61B. α-helices are shown as cylinders and labeled as α1–α7, and β-strands are shown as arrows and labeled as β1–β10. The color scheme corresponds to that of Fig. 2, a gradient from blue (N-terminus) to red (C-terminus).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 383, 144-154) copyright 2008.

Figures were selected by an automated process.