PDBsum entry: 1v0e

Hydrolase

PDB-id: 1v0e

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

666 a.a.

Ligands

PO4 ×6

Waters ×3075

Tools

Clefts Calculation

Biological unit, trimer
- as defined in PDB file (see also PQS)

PDB id:

1v0e

Name:

Hydrolase

Title:

Endosialidase of bacteriophage k1f

Structure:

Endo-alpha-sialidase. Chain: a, b, c, d, e, f. Fragment: catalytic domain, residues 246-911. Synonym: endosialidase. Engineered: yes

Source:

Coliphage k1f. Organism_taxid: 344021. Expressed in: escherichia coli. Expression_system_taxid: 562

Biological unit:

Trimer (from PDB file)

UniProt:

Chains A, B, C, D, E, F: Q858B1 (Q858B1_BPK1F)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

1064 a.a.

Struc:

666 a.a.*

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme class:

E.C.3.2.1.129   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of (2->8)-alpha-sialosyl linkages in oligo- or poly(sialic) acids.

Resolution:

1.9Å

R-factor:

0.167

R-free:

0.202

Authors:

K.Stummeyer,A.Dickmanns,M.Muehlenhoff,R.Gerady-Schahn, R.Ficner

Key ref:

K.Stummeyer et al. (2005). Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F.. Nat Struct Mol Biol, 12, 90-96. [PubMed id: 15608653] [DOI: 10.1038/nsmb874]

Date:

28-Mar-04

Release date:

13-Dec-04

Related entries:

1v0f endosialidase of bacteriophage k1f in complex with oligomeric alpha-2,8-sialic acid

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Key reference

DOI no: 10.1038/nsmb874

Nat Struct Mol Biol 12:90-96 (2005)

PubMed id: 15608653

Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F.

K.Stummeyer, A.Dickmanns, M.Mühlenhoff, R.Gerardy-Schahn, R.Ficner.

ABSTRACT

Phages infecting the polysialic acid (polySia)-encapsulated human pathogen Escherichia coli K1 are equipped with capsule-degrading tailspikes known as endosialidases, which are the only identified enzymes that specifically degrade polySia. As polySia also promotes cellular plasticity and tumor metastasis in vertebrates, endosialidases are widely applied in polySia-related neurosciences and cancer research. Here we report the crystal structures of endosialidase NF and its complex with oligomeric sialic acid. The structure NF, which reveals three distinct domains, indicates that the unique polySia specificity evolved from a combination of structural elements characteristic of exosialidases and bacteriophage tailspike proteins. The endosialidase assembles into a catalytic trimer stabilized by a triple beta-helix. Its active site differs markedly from that of exosialidases, indicating an endosialidase-specific substrate-binding mode and catalytic mechanism. Residues essential for endosialidase activity were identified by structure-based mutational analysis.

Selected figure(s)

Figure 1.
Figure 1. Structure of endoNF (residues 245 -911). (a) Ribbon diagram of one of the endoNF homotrimers present in the asymmetric unit. The three monomers are red, blue and yellow. (b) Structure of the endoNF monomer with its three domains. The chain is colored from blue at the N terminus to red at the C terminus. (c) Bottom view of the homotrimer with cross-section through its triangular tail domain. An 2,8-linked sialic acid dimer bound to the yellow -barrel domain is in stick representation.

Figure 5.
Figure 5. Surface representation of the endoNF homotrimer in complex with sialic acid. The molecular surface of the left trimer is colored by electrostatic potential (blue, positive; red, negative),whereas the transparent surface of the right trimer shows the underlying ribbon model. Sialic acid residues bound to the -barrel as 2,8-linked dimer and as monomer to the -prism domain of the spike are green spheres. Polymeric sialic acid could simultaneously interact with both binding sites, on the spike (yellow monomer) and the -barrel (red monomer) and be cleaved by the active site of the third subunit (blue monomer).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 90-96) copyright 2005.

Figures were selected by an automated process.