PDBsum entry 1sli

Hydrolase

PDB id: 1sli

Contents

Protein chain

679 a.a. *

Ligands

DAN

Waters ×617

* Residue conservation analysis

PDB id:

1sli

Name:

Hydrolase

Title:

Leech intramolecular trans-sialidase complexed with dana

Structure:

Intramolecular trans-sialidase. Chain: a. Fragment: devoid of n-terminal 28 residues. Engineered: yes

Source:

Macrobdella decora. North american leech. Organism_taxid: 6405. Gene: t7. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: de3.

Resolution:

2.00Å R-factor: 0.167 R-free: 0.224

Authors:

Y.Luo,S.C.Li,M.Y.Chou,Y.T.Li,M.Luo

Key ref:

Y.Luo et al. (1998). The crystal structure of an intramolecular trans-sialidase with a NeuAc alpha2-->3Gal specificity. Structure, 6, 521-530. PubMed id: 9562562 DOI: 10.1016/S0969-2126(98)00053-7

Date:

28-Mar-98 Release date: 20-Apr-99

Protein chain

Q27701  (NANL_MACDE) -  Anhydrosialidase from Macrobdella decora

Seq: 762 a.a.

Struc: 679 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.2.15 - anhydrosialidase.
• Pathway: Anhydrosialidase

DOI no: 10.1016/S0969-2126(98)00053-7

Structure 6:521-530 (1998)

PubMed id: 9562562

The crystal structure of an intramolecular trans-sialidase with a NeuAc alpha2-->3Gal specificity.

Y.Luo, S.C.Li, M.Y.Chou, Y.T.Li, M.Luo.

ABSTRACT

BACKGROUND: Intramolecular trans-sialidase from leech (Macrobdella decora) is a unique enzyme which cleaves the terminal neuraminic acid (NeuAc) residue from sialoglycoconjugates, releasing 2, 7-anhydro-neuraminic acid (2,7-anhydro-NeuAc). It is the first enzyme found to exhibit strictly specific cleavage of NeuAc alpha2-->3Gal linkages in sialoglycoconjugates. The release of 2,7-anhydro-NeuAc instead of NeuAc implies a unique mechanism, in which the sialosyl linkage is transferred within the sialoglycoconjugate rather than hydrolyzed. The aims of the structural study were to gain structural insight into the strict specificity and unique mechanism of this unusual enzyme. Results:. The 2.0 A crystal structure of recombinant leech intramolecular trans-sialidase has been solved by multiple isomorphous replacement. The 1.8 A structure of the enzyme in complex with 2-deoxy-2, 3-didehydro-NeuAc was also solved. The refined model comprising residues 81-769 has a catalytic beta-propeller domain (C), a N-terminal lectin-like domain (II) and an irregular beta-stranded domain (III) inserted into the catalytic domain. The structure reveals several possible carbohydrate-binding features: domain II has a concave face, like that of other sialidases, and there is a suitable surface charge distribution at the domain III-C interface. CONCLUSIONS: Structural comparisons showed closer evolutionary relationships to bacterial sialidases than to viral neuraminidases. Mainchain and sidechain atoms around Thr593 make the glycerol-binding pocket incapable of accommodating an extended equatorial 6-glycerol group, implying that the 6-glycerol group of the reaction intermediate may occupy an axial position, which is also required by the catalytic mechanism. The steric hindrance introduced by the bulky sidechain of Trp734 above the 2-carboxylate group may explain the lack of water involvement in the cleavage reaction and the substrate specificity.

Selected figure(s)

Figure 2.
Figure 2. Multidomain architecture of leech IT-sialidase. (a) Ribbon representation of the multidomain structure of leech IT-sialidase. The ordered structure starts with the N-terminal lectin-like domain II in red and continues with the canonical propeller-like catalytic domain C in green. The irregular b-stranded domain III (in blue) is inserted between the two central b strands of the second b sheet of domain C. Neu5Ac2en in the active site is shown as a space-filling model. The suggested carbohydrate-binding residues in the concave face of domain II are shown in ball-and-stick representation. (b,c) Color-coded surface electrostatic potential map (positive in blue, negative in red) of leech IT-sialidase. (b) The face of the active site. (c) The reverse side of the active site.

The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 521-530) copyright 1998.

Figure was selected by an automated process.