PDBsum entry: 1s0i

Hydrolase

PDB-id

1s0i

Contents

Description

Header details

Protein chain

Ligands

SLT

Waters ×590

* Residue conservation analysis

Tools

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PDB id:

1s0i

Name:

Hydrolase

Title:

Trypanosoma cruzi trans-sialidase in complex with sialyl- lactose (michaelis complex)

Structure:

Trans-sialidase. Chain: a. Engineered: yes. Mutation: yes

Source:

Trypanosoma cruzi. Organism_taxid: 5693. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Q26966 (Q26966_TRYCR)

Seq:

Struc:

Seq:

Struc:

Seq:

642 a.a.

Struc:

623 a.a.*

Key:

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 12 residue positions (black crosses)

Resolution:

1.60Å

R-factor:

0.165

R-free:

0.187

Authors:

M.F.Amaya,A.G.Watts,I.Damager,A.Wehenkel,T.Nguyen, A.Buschiazzo,G.Paris,A.C.Frasch,S.G.Withers,P.M.Alzari

Key ref:

M.F.Amaya et al. (2004). Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase.. Structure, 12, 775-784. [PubMed id: 15130470] [DOI: 10.1016/j.str.2004.02.036]

Date:

31-Dec-03

Release date:

18-May-04

Related entries:

1s0j
trypanosoma cruzi trans-sialidase in complex with munana
(michaelis complex)
1s0k
trypanosoma cruzi trans-sialidase in complex with 2,3-
difluoro sialic acid (covalent intermediate)

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CATH

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Key reference

DOI no: 10.1016/j.str.2004.02.036 Structure 12:775-784 (2004)

PubMed id: 15130470

Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase.

M.F.Amaya, A.G.Watts, I.Damager, A.Wehenkel, T.Nguyen, A.Buschiazzo, G.Paris, A.C.Frasch, S.G.Withers, P.M.Alzari.

ABSTRACT

Sialidases are a superfamily of sialic-acid-releasing enzymes that are of significant interest due to their implication as virulence factors in the pathogenesis of a number of diseases. However, extensive studies of viral and microbial sialidases have failed to provide a comprehensive picture of their mechanistic properties, in part because the structures of competent enzyme-substrate complexes and reaction intermediates have never been described. Here we report these structures for the Trypanosoma cruzi trans-sialidase (TcTS), showing that catalysis by sialidases occurs via a similar mechanism to that of other retaining glycosidases, but with some intriguing differences that may have evolved in response to the substrate structure.

Selected figure(s)

Figure 3.
Figure 3. Structure of the Covalent Sialyl-Enzyme Intermediate(A) Chemical structure of 2,3-difluoro-sialic acid used for trapping the reaction intermediate (Watts et al., 2003).(B) Side and top views of the electron density (2Fo-Fc) map for the covalent sialyl-tyrosine adduct (for clarity, Tyr342 has been omitted in the right-hand view).

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 775-784) copyright 2004.

Figure was selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id Reference

19780074 J.H.Kim, H.W.Ryu, J.H.Shim, K.H.Park, and S.G.Withers (2009).
Development of new and selective Trypanosoma cruzi trans-sialidase inhibitors from sulfonamide chalcones and their derivatives.

Chembiochem, 10, 2475-2479.

19269961 R.Carapito, A.Imberty, J.M.Jeltsch, S.C.Byrns, P.H.Tam, T.L.Lowary, A.Varrot, and V.Phalip (2009).
Molecular Basis of Arabinobio-hydrolase Activity in Phytopathogenic Fungi: CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF FUSARIUM GRAMINEARUM GH93 EXO-{alpha}-L-ARABINANASE.

J Biol Chem, 284, 12285-12296.

PDB codes: 2w5n 2w5o

19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.

J Biochem, 146, 61-70.

18949046 L.Ratier, M.Urrutia, G.Paris, L.Zarebski, A.C.Frasch, and F.A.Goldbaum (2008).
Relevance of the diversity among members of the Trypanosoma cruzi trans-sialidase family analyzed with camelids single-domain antibodies.

PLoS ONE, 3, e3524.

18218621 S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, and G.L.Taylor (2008).
The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.

J Biol Chem, 283, 9080-9088.

PDB codes: 2bf6 2vk5 2vk6 2vk7

18019540 V.L.Campo, I.Carvalho, S.Allman, B.G.Davis, and R.A.Field (2007).
Chemical and chemoenzymatic synthesis of glycosyl-amino acids and glycopeptides related to Trypanosoma cruzi mucins.

Org Biomol Chem, 5, 2645-2657.

16819962 J.Mucci, M.G.Risso, M.S.Leguizamón, A.C.Frasch, and O.Campetella (2006).
The trans-sialidase from Trypanosoma cruzi triggers apoptosis by target cell sialylation.

Cell Microbiol, 8, 1086-1095.

16823793 V.A.Money, N.L.Smith, A.Scaffidi, R.V.Stick, H.J.Gilbert, and G.J.Davies (2006).
Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.

Angew Chem Int Ed Engl, 45, 5136-5140.

PDB codes: 2cip 2cit

16206228 J.N.Watson, S.Newstead, A.A.Narine, G.Taylor, and A.J.Bennet (2005).
Two nucleophilic mutants of the Micromonospora viridifaciens sialidase operate with retention of configuration by two different mechanisms.

Chembiochem, 6, 1999-2004.

PDB code: 1wcq

15608653 K.Stummeyer, A.Dickmanns, M.Mühlenhoff, R.Gerardy-Schahn, and R.Ficner (2005).
Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F.

Nat Struct Mol Biol, 12, 90-96.

PDB codes: 1v0e 1v0f

15502328 S.Newstead, C.H.Chien, M.Taylor, and G.Taylor (2004).
Crystallization and atomic resolution X-ray diffraction of the catalytic domain of the large sialidase, nanI, from Clostridium perfringens.

Acta Crystallogr D Biol Crystallogr, 60, 2063-2066.

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.