PDBsum entry: 1ehd

Plant protein

PDB id: 1ehd

Contents

Protein chain

89 a.a. *

Waters ×54

* Residue conservation analysis

PDB id:

1ehd

Name:

Plant protein

Title:

Crystal structure of urtica dioica agglutinin isolectin vi

Structure:

Agglutinin isolectin vi. Chain: a

Source:

Urtica dioica. Great nettle. Organism_taxid: 3501

Resolution:

1.50Å R-factor: 0.229 R-free: 0.267

Authors:

K.Harata,M.Muraki

Key ref:

K.Harata and M.Muraki (2000). Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose. J Mol Biol, 297, 673-681. PubMed id: 10731420 DOI: 10.1006/jmbi.2000.3594

Date:

20-Feb-00 Release date: 05-Apr-00

Protein chain

Q9S7B3  (Q9S7B3_URTDI) -  Agglutinin isolectin V (Precursor)

Seq: 112 a.a.

Struc: 89 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Biological process: cell wall macromolecule catabolic process (2 terms)
• Biochemical function: chitin binding (2 terms)

DOI no: 10.1006/jmbi.2000.3594

J Mol Biol 297:673-681 (2000)

PubMed id: 10731420

Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose.

K.Harata, M.Muraki.

ABSTRACT

Urtica dioica agglutinin is a small plant lectin that binds chitin. We purified the isolectin VI (UDA-VI) and crystal structures of the isolectin and its complex with tri-N-acetylchitotriose (NAG3) were determined by X-ray analysis. The UDA-VI consists of two domains analogous to hevein and the backbone folding of each domain is maintained by four disulfide bridges. The sequence similarity of the two domains is not high (42 %) but their backbone structures are well superimposed except some loop regions. The chitin binding sites are located on the molecular surface at both ends of the dumbbell-shape molecule. The crystal of the NAG3 complex contains two independent molecules forming a protein-sugar 2:2 complex. One NAG3 molecule is sandwiched between two independent UDA-VI molecules and the other sugar molecule is also sandwiched by one UDA-VI molecule and symmetry-related another one. The sugar binding site of N-terminal domain consists of three subsites accommodating NAG3 while two NAG residues are bound to the C-terminal domain. In each sugar-binding site, three aromatic amino acid residues and one serine residue participate to the NAG3 binding. The sugar rings bound to two subsites are stacked to the side-chain groups of tryptophan or histidine and a tyrosine residue is in face-to-face contact with an acetylamino group, to which the hydroxyl group of a serine residue is hydrogen-bonded. The third subsite of the N-terminal domain binds a NAG moiety with hydrogen bonds. The results suggest that the triad of aromatic amino acid residues is intrinsic in sugar binding of hevein-like domains.

Selected figure(s)

Figure 6.
Figure 6. Structures of protein-sugar interaction for two NAG3 molecules. The arrangement of UDA-VI and NAG3 molecules is same as shown in Figure 5. The UDA-VI-1 (blue) and UDA-VI-2 (green). UDA-VI-2' denotes the UDA-VI-2 molecule related by the translation along the c axis. Dotted lines are hydrogen-bonding contacts between UDA-VI and NAG3. Sugar residues are labeled with A, B, and C from the non-reducing end.

Figure 7.
Figure 7. The comparison of the structure of UDA-VI and three fragments consisting of two domains in WGA isolectin 3. The UDA-VI molecule is shown with green color. Structures of domain-1 and 2 (residues 1-86), domain-2 and 3 (residues 44-129), and domain-3 and 4 (residues 87-171) of WGA isolectin 3 (red, yellow, and blue, respectively). The first domains of three WGA fragments are superimposed on the domain-1 of UDA-VI with the r.m.s.d. of 1.09 Å (domain-1), 1.04 Å (domain-2), and 1.09 Å (domain-3) between corresponding C^a atoms.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 673-681) copyright 2000.

Figures were selected by an automated process.