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Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex.

Berke IC, Boehmer T, Blobel G, Schwartz TU - J. Cell Biol. (2004)

Bottom Line: We show that human Nup133 contains two domains: a COOH-terminal domain responsible for its interaction with its subcomplex through Nup107; and an NH2-terminal domain whose crystal structure reveals a seven-bladed beta-propeller.Other beta-propellers are predicted in a third of all nucleoporins.These and several other repeat-based motifs appear to be major elements of nucleoporins, indicating a level of structural repetition that may conceptually simplify the assembly and disassembly of this huge protein complex.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA.

ABSTRACT
Nucleocytoplasmic transport occurs through nuclear pore complexes (NPCs) whose complex architecture is generated from a set of only approximately 30 proteins, termed nucleoporins. Here, we explore the domain structure of Nup133, a nucleoporin in a conserved NPC subcomplex that is crucial for NPC biogenesis and is believed to form part of the NPC scaffold. We show that human Nup133 contains two domains: a COOH-terminal domain responsible for its interaction with its subcomplex through Nup107; and an NH2-terminal domain whose crystal structure reveals a seven-bladed beta-propeller. The surface properties and conservation of the Nup133 beta-propeller suggest it may mediate multiple interactions with other proteins. Other beta-propellers are predicted in a third of all nucleoporins. These and several other repeat-based motifs appear to be major elements of nucleoporins, indicating a level of structural repetition that may conceptually simplify the assembly and disassembly of this huge protein complex.

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Conserved features of the Nup133 NTD propeller. (a) Surface representation showing conservation of residues on the propeller sides. Each view is an ∼120° rotation about the pseudo-sevenfold axis beginning from the NH2 and COOH termini in blade 7 and is the same as in Fig. 2 b. The tube marks the region of the disordered DA34 loop. Conservation scores were calculated using the ConSurf Server (http://consurf.tau.ac.il/) and colored maroon (most conserved) to cyan (most variable). (b) Electrostatic potential of the Nup133 β-propeller. Orientation is as in part a. Red indicates negative regions of the potential and blue indicates positive regions. (c) Sequence alignment of the DA34 loop across representative metazoans. Position of the conserved protein kinase A consensus site is boxed and potential phosphorylated residues are marked by yellow stars. Green triangles mark conserved hydrophobic positions.
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fig4: Conserved features of the Nup133 NTD propeller. (a) Surface representation showing conservation of residues on the propeller sides. Each view is an ∼120° rotation about the pseudo-sevenfold axis beginning from the NH2 and COOH termini in blade 7 and is the same as in Fig. 2 b. The tube marks the region of the disordered DA34 loop. Conservation scores were calculated using the ConSurf Server (http://consurf.tau.ac.il/) and colored maroon (most conserved) to cyan (most variable). (b) Electrostatic potential of the Nup133 β-propeller. Orientation is as in part a. Red indicates negative regions of the potential and blue indicates positive regions. (c) Sequence alignment of the DA34 loop across representative metazoans. Position of the conserved protein kinase A consensus site is boxed and potential phosphorylated residues are marked by yellow stars. Green triangles mark conserved hydrophobic positions.

Mentions: Proteins with the β-propeller fold have diverse functions ranging from catalysis, intra- and extracellular signaling, vesicular sorting, and DNA binding (Paoli, 2001). The wide range of functional possibilities for this fold reflects the variety of interaction surfaces in the β-propeller scaffold: top and bottom surfaces are composed of variable loops that can serve as a docking platform for other proteins; the side surface is composed of grooves at the β-sheet interfaces often involved in peptide interactions; and the inner cavity potentially provides a space for sequestering ligands from bulk solvent. The lack of structural constraints on the evolution of a β-propeller's primary sequence makes this an extremely adaptable module. Mapping the conservation of Nup133 NTDs from six vertebrate species, two insects, and two worms on the hNup133 propeller surface reveals conserved patches that extend along its circumference from blade 5 through blade 2 (Fig. 4 a, left and middle; and Fig. S1, alignment, available at http://www.jcb.org/cgi/content/full/jcb.200408109/DC1). The interface between blade 5 and α2-3 forms a conserved groove that is flanked at either end by negative charges (Fig. 4, a and b). The strongest surface conservation is centered on the α1 insert and a conserved hydrophobic groove runs between α1 and blade 7 (Fig. 4 a). Rotating around the pseudo-sevenfold axis of the propeller, a long disordered but conserved loop (DA34) follows strand 3D (Fig. 4 a, tube representation; and Fig. 4 c, sequence alignment). The loop lies above the entrance to a pocket in the interface between blades 3 and 4 (Fig. 4 b, right).


Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex.

Berke IC, Boehmer T, Blobel G, Schwartz TU - J. Cell Biol. (2004)

Conserved features of the Nup133 NTD propeller. (a) Surface representation showing conservation of residues on the propeller sides. Each view is an ∼120° rotation about the pseudo-sevenfold axis beginning from the NH2 and COOH termini in blade 7 and is the same as in Fig. 2 b. The tube marks the region of the disordered DA34 loop. Conservation scores were calculated using the ConSurf Server (http://consurf.tau.ac.il/) and colored maroon (most conserved) to cyan (most variable). (b) Electrostatic potential of the Nup133 β-propeller. Orientation is as in part a. Red indicates negative regions of the potential and blue indicates positive regions. (c) Sequence alignment of the DA34 loop across representative metazoans. Position of the conserved protein kinase A consensus site is boxed and potential phosphorylated residues are marked by yellow stars. Green triangles mark conserved hydrophobic positions.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2172596&req=5

fig4: Conserved features of the Nup133 NTD propeller. (a) Surface representation showing conservation of residues on the propeller sides. Each view is an ∼120° rotation about the pseudo-sevenfold axis beginning from the NH2 and COOH termini in blade 7 and is the same as in Fig. 2 b. The tube marks the region of the disordered DA34 loop. Conservation scores were calculated using the ConSurf Server (http://consurf.tau.ac.il/) and colored maroon (most conserved) to cyan (most variable). (b) Electrostatic potential of the Nup133 β-propeller. Orientation is as in part a. Red indicates negative regions of the potential and blue indicates positive regions. (c) Sequence alignment of the DA34 loop across representative metazoans. Position of the conserved protein kinase A consensus site is boxed and potential phosphorylated residues are marked by yellow stars. Green triangles mark conserved hydrophobic positions.
Mentions: Proteins with the β-propeller fold have diverse functions ranging from catalysis, intra- and extracellular signaling, vesicular sorting, and DNA binding (Paoli, 2001). The wide range of functional possibilities for this fold reflects the variety of interaction surfaces in the β-propeller scaffold: top and bottom surfaces are composed of variable loops that can serve as a docking platform for other proteins; the side surface is composed of grooves at the β-sheet interfaces often involved in peptide interactions; and the inner cavity potentially provides a space for sequestering ligands from bulk solvent. The lack of structural constraints on the evolution of a β-propeller's primary sequence makes this an extremely adaptable module. Mapping the conservation of Nup133 NTDs from six vertebrate species, two insects, and two worms on the hNup133 propeller surface reveals conserved patches that extend along its circumference from blade 5 through blade 2 (Fig. 4 a, left and middle; and Fig. S1, alignment, available at http://www.jcb.org/cgi/content/full/jcb.200408109/DC1). The interface between blade 5 and α2-3 forms a conserved groove that is flanked at either end by negative charges (Fig. 4, a and b). The strongest surface conservation is centered on the α1 insert and a conserved hydrophobic groove runs between α1 and blade 7 (Fig. 4 a). Rotating around the pseudo-sevenfold axis of the propeller, a long disordered but conserved loop (DA34) follows strand 3D (Fig. 4 a, tube representation; and Fig. 4 c, sequence alignment). The loop lies above the entrance to a pocket in the interface between blades 3 and 4 (Fig. 4 b, right).

Bottom Line: We show that human Nup133 contains two domains: a COOH-terminal domain responsible for its interaction with its subcomplex through Nup107; and an NH2-terminal domain whose crystal structure reveals a seven-bladed beta-propeller.Other beta-propellers are predicted in a third of all nucleoporins.These and several other repeat-based motifs appear to be major elements of nucleoporins, indicating a level of structural repetition that may conceptually simplify the assembly and disassembly of this huge protein complex.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA.

ABSTRACT
Nucleocytoplasmic transport occurs through nuclear pore complexes (NPCs) whose complex architecture is generated from a set of only approximately 30 proteins, termed nucleoporins. Here, we explore the domain structure of Nup133, a nucleoporin in a conserved NPC subcomplex that is crucial for NPC biogenesis and is believed to form part of the NPC scaffold. We show that human Nup133 contains two domains: a COOH-terminal domain responsible for its interaction with its subcomplex through Nup107; and an NH2-terminal domain whose crystal structure reveals a seven-bladed beta-propeller. The surface properties and conservation of the Nup133 beta-propeller suggest it may mediate multiple interactions with other proteins. Other beta-propellers are predicted in a third of all nucleoporins. These and several other repeat-based motifs appear to be major elements of nucleoporins, indicating a level of structural repetition that may conceptually simplify the assembly and disassembly of this huge protein complex.

Show MeSH