PDBsum entry: 1umz

Transferase

PDB-id

1umz

Contents

Description

Header details

Protein chains

Ligands

NAG-NAG-BMA ×2

BGC-BGC-BGC-XYS-
XYS-GAL ×2

Waters ×245

* Residue conservation analysis

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PDB id:

1umz

Name:

Transferase

Title:

Xyloglucan endotransglycosylase in complex with the xyloglucan nonasaccharide xllg.

Structure:

Xyloglucan endotransglycosylase. Chain: a, b. Engineered: yes

Source:

Populus tremula. European aspen. Organism_taxid: 113636. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

UniProt:

Chains A, B: Q8GZD5 (Q8GZD5_9ROSI)

Seq:

Struc:

Seq:

294 a.a.

Struc:

267 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Enzyme class:

E.C.2.4.1.207 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Breaks a beta-(1->4) bond in the backbone of a xyloglucan and transfers the xyloglucanyl segment on to O-4 of the non-reducing terminal glucose residue of an acceptor, which can be a xyloglucan or an oligosaccharide of xyloglucan.

Resolution:

1.8Å

R-factor:

0.203

R-free:

0.222

Authors:

P.Johansson,H.Brumer,A.M.Kallas,H.Henriksson,S.E.Denman, T.T.Teeri,T.A.Jones

Key ref:

P.Johansson et al. (2004). Crystal structures of a poplar xyloglucan endotransglycosylase reveal details of transglycosylation acceptor binding.. Plant Cell, 16, 874-886. [PubMed id: 15020748] [DOI: 10.1105/tpc.020065]

Date:

03-Sep-03

Release date:

18-Mar-04

Related entries:

1un1 xyloglucan endotransglycosylase native structure

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Key reference

DOI no: 10.1105/tpc.020065 Plant Cell 16:874-886 (2004)

PubMed id: 15020748

Crystal structures of a poplar xyloglucan endotransglycosylase reveal details of transglycosylation acceptor binding.

P.Johansson, H.Brumer, M.J.Baumann, A.M.Kallas, H.Henriksson, S.E.Denman, T.T.Teeri, T.A.Jones.

ABSTRACT

Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls via a transglycosylation mechanism. Thus, XET is a key enzyme in all plant processes that require cell wall remodeling. To provide a basis for detailed structure-function studies, the crystal structure of Populus tremula x tremuloides XET16A (PttXET16A), heterologously expressed in Pichia pastoris, has been determined at 1.8-A resolution. Even though the overall structure of PttXET16A is a curved beta-sandwich similar to other enzymes in the glycoside hydrolase family GH16, parts of its substrate binding cleft are more reminiscent of the distantly related family GH7. In addition, XET has a C-terminal extension that packs against the conserved core, providing an additional beta-strand and a short alpha-helix. The structure of XET in complex with a xyloglucan nonasaccharide, XLLG, reveals a very favorable acceptor binding site, which is a necessary but not sufficient prerequisite for transglycosylation. Biochemical data imply that the enzyme requires sugar residues in both acceptor and donor sites to properly orient the glycosidic bond relative to the catalytic residues.

Literature references that cite this PDB file's key reference

PubMed id Reference

19635745 A.Maris, D.Suslov, S.C.Fry, J.P.Verbelen, and K.Vissenberg (2009).
Enzymic characterization of two recombinant xyloglucan endotransglucosylase/hydrolase (XTH) proteins of Arabidopsis and their effect on root growth and cell wall extension.

J Exp Bot, 60, 3959-3972.

19189377 B.Mertz, X.Gu, and P.J.Reilly (2009).
Analysis of functional divergence within two structurally related glycoside hydrolase families.

Biopolymers, 91, 478-495.

19076217 M.Hrmova, V.Farkas, A.J.Harvey, J.Lahnstein, B.Wischmann, N.Kaewthai, I.Ezcurra, T.T.Teeri, and G.B.Fincher (2009).
Substrate specificity and catalytic mechanism of a xyloglucan xyloglucosyl transferase HvXET6 from barley (Hordeum vulgare L.).

FEBS J, 276, 437-456.

19097997 R.Hurtado-Guerrero, A.W.Schüttelkopf, I.Mouyna, A.F.Ibrahim, S.Shepherd, T.Fontaine, J.P.Latgé, and D.M.van Aalten (2009).
Molecular mechanisms of yeast cell wall glucan remodeling.

J Biol Chem, 284, 8461-8469.

PDB codes: 2w61 2w62 2w63

19454593 R.Schröder, R.G.Atkinson, and R.J.Redgwell (2009).
Re-interpreting the role of endo-beta-mannanases as mannan endotransglycosylase/hydrolases in the plant cell wall.

Ann Bot (Lond), 104, 197-204.

19504047 X.Lu, Y.Chu, Q.Wu, Y.Gu, F.Han, and W.Yu (2009).
Cloning, expression and characterization of a new agarase-encoding gene from marine Pseudoalteromonas sp.

Biotechnol Lett, 31, 1565-1570.

18483816 C.Zhou, A.N.Lakso, T.L.Robinson, and S.Gan (2008).
Isolation and characterization of genes associated with shade-induced apple abscission.

Mol Genet Genomics, 280, 83-92.

18040711 T.Takeda, J.G.Miller, and S.C.Fry (2008).
Anionic derivatives of xyloglucan function as acceptor but not donor substrates for xyloglucan endotransglucosylase activity.

Planta, 227, 893-905.

18043802 K.Piens, A.M.Henriksson, F.Gullfot, M.Lopez, R.Fauré, F.M.Ibatullin, T.T.Teeri, H.Driguez, and H.Brumer (2007).
Glycosynthase activity of hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 nucleophile mutants.

Org Biomol Chem, 5, 3971-3978.

17504814 N.Nishikubo, T.Awano, A.Banasiak, V.Bourquin, F.Ibatullin, R.Funada, H.Brumer, T.T.Teeri, T.Hayashi, B.Sundberg, and E.J.Mellerowicz (2007).
Xyloglucan endo-transglycosylase (XET) functions in gelatinous layers of tension wood fibers in poplar--a glimpse into the mechanism of the balancing act of trees.

Plant Cell Physiol, 48, 843-855.

16550377 G.Michel, P.Nyval-Collen, T.Barbeyron, M.Czjzek, and W.Helbert (2006).
Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases.

Appl Microbiol Biotechnol, 71, 23-33.

17057348 J.Vasur, R.Kawai, A.M.Larsson, K.Igarashi, M.Sandgren, M.Samejima, and J.Ståhlberg (2006).
X-ray crystallographic native sulfur SAD structure determination of laminarinase Lam16A from Phanerochaete chrysosporium.

Acta Crystallogr D Biol Crystallogr, 62, 1422-1429.

PDB code: 2cl2

17006642 K.N.Neustroev, A.M.Golubev, M.L.Sinnott, R.Borriss, M.Krah, H.Brumer, E.V.Eneyskaya, S.Shishlyannikov, K.A.Shabalin, V.T.Peshechonov, V.G.Korolev, and A.A.Kulminskaya (2006).
Transferase and hydrolytic activities of the laminarinase from Rhodothermus marinus and its M133A, M133C, and M133W mutants.

Glycoconj J, 23, 501-511.

16774648 M.Saladié, J.K.Rose, D.J.Cosgrove, and C.Catalá (2006).
Characterization of a new xyloglucan endotransglucosylase/hydrolase (XTH) from ripening tomato fruit and implications for the diverse modes of enzymic action.

Plant J, 47, 282-295.

17177793 N.Farrokhi, R.A.Burton, L.Brownfield, M.Hrmova, S.M.Wilson, A.Bacic, and G.B.Fincher (2006).
Plant cell wall biosynthesis: genetic, biochemical and functional genomics approaches to the identification of key genes.

Plant Biotechnol J, 4, 145-167.

16374635 R.Kawai, K.Igarashi, M.Yoshida, M.Kitaoka, and M.Samejima (2006).
Hydrolysis of beta-1,3/1,6-glucan by glycoside hydrolase family 16 endo-1,3(4)-beta-glucanase from the basidiomycete Phanerochaete chrysosporium.

Appl Microbiol Biotechnol, 71, 898-906.

15557263 M.Strohmeier, M.Hrmova, M.Fischer, A.J.Harvey, G.B.Fincher, and J.Pleiss (2004).
Molecular modeling of family GH16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae.

Protein Sci, 13, 3200-3213.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.