PDBsum entry: 2vh9

Hydrolase

PDB id: 2vh9

Contents

Protein chains

266 a.a. *

Ligands

GOL ×2

BGC-BGC-BGC-BGC-XYS-GAL-XYS-GAL-XYS ×2

Metals

_ZN ×2

Waters ×515

* Residue conservation analysis

PDB id:

2vh9

Name:

Hydrolase

Title:

Crystal structure of nxg1-deltayniig in complex with xllg, a xyloglucan derived oligosaccharide

Structure:

Cellulase. Chain: a, b. Synonym: xyloglucan hydrolase. Engineered: yes

Source:

Tropaeolum majus. Nasturtium. Organism_taxid: 4020. Tissue: seedling. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

2.10Å R-factor: 0.151 R-free: 0.203

Authors:

M.Czjzek,P.Mark,M.J.Baumann,J.M.Eklof,G.Michel,H.Brumer

Key ref:

P.Mark et al. (2008). Analysis of nasturtium TmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucan endo-transglycosylases and endo-hydrolases. Proteins, 75, 820-836. PubMed id: 19004021 DOI: 10.1002/prot.22291

Date:

20-Nov-07 Release date: 25-Nov-08

Protein chains

Q07524  (Q07524_TROMA) -  Cellulase

Seq: 295 a.a.

Struc: 266 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.4 - Cellulase.
• Reaction: Endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.

 Gene Ontology (GO) functional annotation 

• Cellular component: apoplast (2 terms)
• Biological process: metabolic process (3 terms)
• Biochemical function: hydrolase activity (5 terms)

DOI no: 10.1002/prot.22291

Proteins 75:820-836 (2008)

PubMed id: 19004021

Analysis of nasturtium TmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucan endo-transglycosylases and endo-hydrolases.

P.Mark, M.J.Baumann, J.M.Eklöf, F.Gullfot, G.Michel, A.M.Kallas, T.T.Teeri, H.Brumer, M.Czjzek.

ABSTRACT

Reorganization and degradation of the wall crosslinking and seed storage polysaccharide xyloglucan by glycoside hydrolase family 16 (GH16) endo-transglycosylases and hydrolases are crucial to the growth of the majority of land plants, affecting processes as diverse as germination, morphogenesis, and fruit ripening. A high-resolution, three-dimensional structure of a nasturtium (Tropaeolum majus) endo-xyloglucanase loop mutant, TmNXG1-DeltaYNIIG, with an oligosaccharide product bound in the negative active-site subsites, has been solved by X-ray crystallography. Comparison of this novel complex to that of the strict xyloglucan endo-transglycosylase PttXET16-34 from hybrid aspen (Populus tremula x tremuloides), previously solved with a xylogluco-oligosaccharide bound in the positive subsites, highlighted key protein structures that affect the disparate catalytic activities displayed by these closely related enzymes. Combination of these "partial" active-site complexes through molecular dynamics simulations in water allowed modeling of wild-type TmNXG1, TmNXG1-DeltaYNIIG, and wild-type PttXET16-34 in complex with a xyloglucan octadecasaccharide spanning the entire catalytic cleft. A comprehensive analysis of these full-length complexes underscored the importance of various loops lining the active site. Subtle differences leading to a tighter hydrogen bonding pattern on the negative (glycosyl donor) binding subsites, together with loop flexibility on the positive (glycosyl acceptor) binding subsites appear to favor hydrolysis over transglycosylation in GH16 xyloglucan-active enzymes. Proteins 2009. (c) 2008 Wiley-Liss, Inc.

Selected figure(s)

Figure 3.
Figure 3. Structural representation of TmNXG1- YNIIG in complex with a XLLG molecule bound to the donor sub binding sites -4 to -1. (a) Cross-eyed stereo surface representation of the active site cleft on the donor side. The XLLG molecule is represented as sticks. The sub binding sites from -4 to -1 are indicated, as well as the positions of loops 1, 2 and 3. (b) Ribbon representation of the two symmetric molecules in the crystal structure of TmNXG1- YNIIG in complex with XLLG. Molecule A is colored in green and molecule B in blue. The substrate molecules are in stick representation. The sugar bound to molecule A is colored with yellow carbon atoms and red oxygen atoms, and the sugar bound to molecule B with light blue carbon atoms and red oxygen atoms.

Figure 5.
Figure 5. Surface representations of the modeled complexes obtained after MD calculations for PttXET16-34 and TmNXG1 molecules in complex with a XLLG-XLLG substrate molecule spanning the entire active site cleft from -4 to +4. (a) Front view of the complex model TmNXG1 with XLLG-XLLG; (b) perpendicular view [90° with respect to (a)] of the complex model TmNXG1 with XLLG-XLLG; (c) front view of the complex model PttXET16-34 with XLLG-XLLG; and (d) perpendicular view [90° with respect to (c)] of the complex model PttXET16-34 with XLLG-XLLG.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 75, 820-836) copyright 2008.

Figures were selected by the author.