Crystal structure of the polysialic acid–degrading endosialidase of bacteriophage K1F

Stummeyer, Katharina; Dickmanns, Achim; Mühlenhoff, Martina; Gerardy‐Schahn, Rita; Ficner, Ralf

doi:10.1038/nsmb874

Cited by 180 publications

(242 citation statements)

References 50 publications

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“…2) shows two clearly distinct domains, the fully folded triple-β-helix stalk and the chaperone domain. The stalk domain essentially adopts the fold of an intertwined triple β-helix, which was previously described 7 , whereas the chaperone domain adopts the same architecture found for GP12-CIMCD (see above). A central twisted three-helix bundle (α4) of 35 Å length, surrounded by α-helices and two short antiparallel β-strands (α1-β1-α2-β2-α3-α3a) forms the core with an approximate diameter of 50 Å.…”

Section: A R T I C L E S a R T I C L E Ssupporting

confidence: 56%

“…Furthermore, it could be shown that some of the chaperone domains are exchangeable between the different preproteins 5,6 . While the three-dimensional structures of the CIMCDs are as yet unknown, the crystal structure of N-terminally truncated mature endoNF shows that the homotrimeric enzyme comprises a triple β-helix involved in substrate recognition 7 . This triple β-helix and the related triple-β-spiral motif have been identified in various proteins, which often play a role as virulence factors 8 .…”

Section: A R T I C L E Smentioning

confidence: 99%

“…In order to gain insight into the details of the cleavage reaction and the structural basis for CIMCD-mediated folding, the interaction between the CIMCD and the pre-protein needed to be examined. Because a noncleavable mutant of GP12 (GP12 S620A ) failed to crystallize, we designed a truncated version of a noncleavable mutant of endoNF (endoNF S911A ), containing the triple β-helix but lacking the N-terminal catalytic sialidase domain, based on the threedimensional structure of endoNF 5,7 .…”

Section: Structure Of Gp12-cimcdmentioning

confidence: 99%

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Crystal structure of an intramolecular chaperone mediating triple–β-helix folding

Schulz

Dickmanns

Urlaub

et al. 2010

Nat Struct Mol Biol

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106

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Proteins fold into their functional three-dimensional structure based on the information encoded in the residue sequence 1 . In all domains of life, various strategies evolved to assist folding processes in order to prevent immediate misfolding and aggregation of the nascent polypeptide chain. In the crowded cellular environment, protein folding is often aided by molecular chaperones. Molecular chaperones differ in size, function and energy dependence; however, all have in common to bind to the unfolded state of the protein in order to facilitate or mediate assembly of the correct three-dimensional structure 2,3 . In contrast to molecular chaperones, the intramolecular chaperones (IMCs) constitute a different class of chaperones. As part of the polypeptide chain, the IMC is typically cleaved off the target protein after the folding process is completed. Two classes of IMCs can be distinguished: class I IMCs assist the protein to fold into the correct tertiary structure, whereas class II IMCs are involved in quaternary structure assembly 4 . In contrast to many molecular chaperones, no evidence for an ATP-driven cleavage reaction could be found in IMCs. An example of a class II intramolecular chaperone has been identified in viral tailspike and fiber proteins. These proteins are functionally unrelated but share a highly conserved chaperone domain at their C terminus (C-terminal intramolecular chaperone domain, CIMCD), which is cleaved at a conserved position in an autoproteolytic reaction 5 . It was shown that the covalent linkage between the CIMCD and N-terminal pre-protein is necessary for correct folding, indicating that an in trans function of the chaperone is impossible 5 . Furthermore, it could be shown that some of the chaperone domains are exchangeable between the different preproteins 5,6 . While the three-dimensional structures of the CIMCDs are as yet unknown, the crystal structure of N-terminally truncated mature endoNF shows that the homotrimeric enzyme comprises a triple β-helix involved in substrate recognition 7 . This triple β-helix and the related triple-β-spiral motif have been identified in various proteins, which often play a role as virulence factors 8 . In triple β-helices, three polypeptide chains wind around a common threefold symmetry axis, conferring an extraordinary stability to the protein. The rigid elongated shape allows triple β-helix-comprising proteins to protrude from a pathogen's surface in order to interact with flexible host cell receptors, like lipopolysaccharides 9 . However, proper assembly of triple-β-helical folds poses to be difficult in the absence of a trimerization domain 10 . Hence, most triple β-helices depend on a C-terminal extension for trimerization and correct assembly 11 .Here we present the crystal structures of two representatives of a large group of systematically, functionally and structurally similar intramolecular chaperones: the Escherichia coli phage K1F endosilidase CIMCD and the Bacillus subtilis phage GA-1 neck appendage protein CIMCD. Furthermore...

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Section: A R T I C L E S a R T I C L E Ssupporting

confidence: 56%

Section: A R T I C L E Smentioning

confidence: 99%

Section: Structure Of Gp12-cimcdmentioning

confidence: 99%

See 1 more Smart Citation

Crystal structure of an intramolecular chaperone mediating triple–β-helix folding

Schulz

Dickmanns

Urlaub

et al. 2010

Nat Struct Mol Biol

Self Cite

106

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“…Comparable structures include the triple β-helix regions of phage T4 gp12 (41) and gp5 (42), the K1F endosialidase (43) and endo-N-acetylneuramidase (29), streptococcal (pro)phage HylP1 and Hylp2 (44,45), the phage P22 cell penetrating needle gp26 (40), and phage Phi29 tail-spike (46). However, the most similar structures are those of phage P2 gpV (Fig.…”

Section: Discussionmentioning

confidence: 99%

Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers

Garcia-Doval

Raaij

2012

Proc. Natl. Acad. Sci. U.S.A.

104

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The six bacteriophage T7 tail fibers, homo-trimers of gene product 17, are thought to be responsible for the first specific, albeit reversible, attachment to Escherichia coli lipopolysaccharide. The protein trimer forms kinked fibers comprised of an amino-terminal tail-attachment domain, a slender shaft, and a carboxyl-terminal domain composed of several nodules. Previously, we expressed, purified, and crystallized a carboxyl-terminal fragment comprising residues 371-553. Here, we report the structure of this protein trimer, solved using anomalous diffraction and refined at 2 Å resolution. Amino acids 371-447 form a tapered pyramid with a triangular cross-section composed of interlocked β-sheets from each of the three chains. The triangular pyramid domain has three α-helices at its narrow end, which are connected to a carboxyl-terminal three-blade β-propeller tip domain by flexible loops. The monomers of this tip domain each contain an eight-stranded β-sandwich. The exact topology of the β-sandwich fold is novel, but similar to that of knob domains of other viral fibers and the phage Sf6 needle. Several host-range change mutants have been mapped to loops located on the top of this tip domain, suggesting that this surface of the tip domain interacts with receptors on the cell surface.bacterial viruses | caudovirales | crystallography | infection | Podoviridae B acteriophages (bacterial viruses or phages) are important biological model systems and, because of the high specificity for their host bacteria, have found application in phage typing, food security, and phage therapy (1). Escherichia coli phage T7 is a member of the Podoviridae family of the Caudovirales (tailed phages) order (2). T7 is composed of an icosahedral capsid with a 20-nm short tail at one of the vertices (3, 4). The capsid is formed by the shell protein gene product (gp) 10 and encloses a DNA of 40 kb. A cylindrical structure composed of gp14, gp15, and gp16 is present inside the capsid (5), attached to the special vertex formed by the connector, a circular dodecamer of gp8 (6). Gp11 and gp12 form the tail; gp13, gp6.7, and gp7.3 have also been shown to be part of the virion and to be necessary for infection, although their location has not been established (7,8). Although extensive electron microscopy studies have been performed on phage T7 (3-6, 9), crystallographic studies have so far been limited to its nonstructural proteins.The main portion of the tail is composed of gp12, a large protein of which six copies are present (10); the small gp11 protein is also located in the tail (5). Attached to the tail are six fibers, each containing three copies of the gp17 protein. T7 tail fibers are elongated homo-trimers, which are responsible for initial, reversible, host cell recognition. A second, irreversible, decisionmaking interaction with the bacterial membrane is presumably mediated by one or more of the tail-tube proteins. DNA transfer into the host is then mediated by an extension formed by gp14-16 (7, 8, 11). Previously, we have reported t...

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“…Other top structural homologs are the human UPF1 human helicase core (Z score ϭ 5.1, 1 st ) (21), the ␤-barrel domain of endo-alpha-sialidase (22), the tRNA-binding domain of the translation elongation factor Tu (23), and the receptor-binding domain of the avian reovirus fiber C (24). Of these top homologs, the endosialidase of bacteriophage K1F is most interesting due to its ability to bind sialic acid molecules, which are widely distributed in animal tissues and bacteria (22) (Fig. 2C).…”

Section: Resultsmentioning

confidence: 99%

Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding

Guu

Liu

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

220

247

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Hepatitis E virus (HEV), a small, non-enveloped RNA virus in the familyHepeviridae, is associated with endemic and epidemic acute viral hepatitis in developing countries. Our 3.5-Å structure of a HEV-like particle (VLP) shows that each capsid protein contains 3 linear domains that form distinct structural elements: S, the continuous capsid; P1, 3-fold protrusions; and P2, 2-fold spikes. The S domain adopts a jelly-roll fold commonly observed in small RNA viruses. The P1 and P2 domains both adopt ␤-barrel folds. Each domain possesses a potential polysaccharide-binding site that may function in cell-receptor binding. Sugar binding to P1 at the capsid protein interface may lead to capsid disassembly and cell entry. Structural modeling indicates that native T ‫؍‬ 3 capsid contains flat dimers, with less curvature than those of T ‫؍‬ 1 VLP. Our findings significantly advance the understanding of HEV molecular biology and have application to the development of vaccines and antiviral medications.capsid ͉ HEV V iral hepatitis is principally caused by 5 distinct viruses named hepatitis A-E. Despite their similar names, the 5 viruses are unrelated, and they have totally different genome structures with distinct replication mechanisms. Hepatitis E virus (HEV) is responsible for endemic hepatitis as well as sporadic epidemics of acute, enterically transmitted hepatitis in the developing world, including parts of Asia, the Middle East, Africa, and Mexico (1, 2). HEV accounts for more than 50% of acute viral hepatitides in young adults in these regions, with a case fatality of 1-2% in regular patients and up to 20% in pregnant women.Given the lack of a robust cell culture system, and because HEV is not closely related to any other well-characterized virus, little is known about the molecular biology of HEV or its strategy for replication (1). HEV is a small, non-enveloped virus with a 7.2 kb, positive-sense RNA genome. Its genomic RNA is polyadenylated and contains 3 ORFs. Located near the 5Ј-end, ORF1 encodes a non-structural polyprotein with multiple functional domains, including those for methyltransferase, protease, helicase, and polymerase. The viral capsid protein (CP) is encoded by ORF2 near the 3Ј-end. ORF3, which partially overlaps with the other 2 ORFs, codes for an immunogenic protein of unknown function. HEV was originally classified in the Caliciviridae family because of its structural similarity to other caliciviruses; however, it is now the sole member of the Hepeviridae family. The genomic RNA of HEV exhibits several distinct features compared to the genomic RNA of caliciviruses, including a methylated cap at the 5Ј-end and an ORF1 with functional domains arranged in a different order (1, 3).Previous studies of HEV assembly have primarily focused on the overexpression of viral proteins. The ORF2 capsid protein, HEV-CP, contains a total of 660 amino acid residues. At the HEV-CP N terminus is a signal peptide followed by an arginine-rich domain that potentially play a role in viral RNA encapsidation during assem...

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Crystal structure of the polysialic acid–degrading endosialidase of bacteriophage K1F

Cited by 180 publications

References 50 publications

Crystal structure of an intramolecular chaperone mediating triple–β-helix folding

Crystal structure of an intramolecular chaperone mediating triple–β-helix folding

Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers

Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding

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