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Consensus nomenclature for the human ArfGAP domain-containing proteins.

Kahn RA, Bruford E, Inoue H, Logsdon JM, Nie Z, Premont RT, Randazzo PA, Satake M, Theibert AB, Zapp ML, Cassel D - J. Cell Biol. (2008)

Bottom Line: At the FASEB summer research conference on "Arf Family GTPases", held in Il Ciocco, Italy in June, 2007, it became evident to researchers that our understanding of the family of Arf GTPase activating proteins (ArfGAPs) has grown exponentially in recent years.Nearly 100 researchers were contacted to generate a consensus nomenclature for human ArfGAPs.This article describes the resulting consensus nomenclature and provides a brief description of each of the 10 subfamilies of 31 human genes encoding proteins containing the ArfGAP domain.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA. rkahn@emory.edu

ABSTRACT
At the FASEB summer research conference on "Arf Family GTPases", held in Il Ciocco, Italy in June, 2007, it became evident to researchers that our understanding of the family of Arf GTPase activating proteins (ArfGAPs) has grown exponentially in recent years. A common nomenclature for these genes and proteins will facilitate discovery of biological functions and possible connections to pathogenesis. Nearly 100 researchers were contacted to generate a consensus nomenclature for human ArfGAPs. This article describes the resulting consensus nomenclature and provides a brief description of each of the 10 subfamilies of 31 human genes encoding proteins containing the ArfGAP domain.

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Related in: MedlinePlus

Domain organization of human ArfGAP subfamilies and structure of the ArfGAP domain. (A) Representative domain structures of each human ArfGAP subfamily are depicted and are drawn to scale. Abbreviations are: ALPS, ArfGAP1 lipid-packing sensor; ArfGAP, ArfGAP domain; ANK, ankyrin repeat; BAR, Bin/Amphiphysin/Rvs; CALM, CALM binding domain; CB, clathrin-box; CC, coiled-coil; FG repeats, multiple copies of the XXFG motif; GLD, GTP-binding protein-like domain; PBS, Paxillin binding site; PH, pleckstrin homology domain; Pro(PxxP)3, cluster of three Proline-rich (PxxP) motifs; Pro(D/ELPPKP)8, eight tandem Proline-rich (D/ELPPKP) motifs; RA, Ras association motif; RhoGAP, RhoGAP domain; SAM, sterile α-motif; SH3, Src homology 3 domain; SHD, Spa-homology domain. Notes: (1) SMAP2 has CALM BD, but SMAP1 does not. (2) ASAP1 contains the indicated Pro-rich domains; ASAP2 and ASAP3 lack the Pro (D/ELPPKP) repeat and ASAP3 does not have an SH3 domain. (3) AGAP2 has a splice variant with three N-terminal PxxP motifs, called PIKE-L. (B) The structure of the isolated ArfGAP domain of human ArfGAP1 (residues 6–120) is displayed with the backbone shown in green with secondary structures indicated. The side chains of only the conserved arginine (Arg50, on the right) and the four zinc finger cysteines (center; Cys22, 25, 42, and 45) are displayed along with the coordinated Zn2+ (gray sphere). This image was generated using PyMol.
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fig1: Domain organization of human ArfGAP subfamilies and structure of the ArfGAP domain. (A) Representative domain structures of each human ArfGAP subfamily are depicted and are drawn to scale. Abbreviations are: ALPS, ArfGAP1 lipid-packing sensor; ArfGAP, ArfGAP domain; ANK, ankyrin repeat; BAR, Bin/Amphiphysin/Rvs; CALM, CALM binding domain; CB, clathrin-box; CC, coiled-coil; FG repeats, multiple copies of the XXFG motif; GLD, GTP-binding protein-like domain; PBS, Paxillin binding site; PH, pleckstrin homology domain; Pro(PxxP)3, cluster of three Proline-rich (PxxP) motifs; Pro(D/ELPPKP)8, eight tandem Proline-rich (D/ELPPKP) motifs; RA, Ras association motif; RhoGAP, RhoGAP domain; SAM, sterile α-motif; SH3, Src homology 3 domain; SHD, Spa-homology domain. Notes: (1) SMAP2 has CALM BD, but SMAP1 does not. (2) ASAP1 contains the indicated Pro-rich domains; ASAP2 and ASAP3 lack the Pro (D/ELPPKP) repeat and ASAP3 does not have an SH3 domain. (3) AGAP2 has a splice variant with three N-terminal PxxP motifs, called PIKE-L. (B) The structure of the isolated ArfGAP domain of human ArfGAP1 (residues 6–120) is displayed with the backbone shown in green with secondary structures indicated. The side chains of only the conserved arginine (Arg50, on the right) and the four zinc finger cysteines (center; Cys22, 25, 42, and 45) are displayed along with the coordinated Zn2+ (gray sphere). This image was generated using PyMol.

Mentions: ArfGAPs are a family of proteins containing a characteristic module, the ArfGAP domain, which was first identified in rat ArfGAP1 as the domain responsible for stimulation of GTP hydrolysis on Arf1 (Cukierman et al., 1995). ArfGAP domains are ancient and highly conserved since the earliest eukaryotes. Five ArfGAPs have been identified in the yeast Saccharomyces cerevisiae and shown to display a combination of redundant and unique functions. Mammalian cells express an array of ArfGAPs ranging from relatively small proteins resembling those found in yeast to the large, multi-domain ArfGAPs that are proposed to function as scaffolds for cell signaling (Fig. 1 A).


Consensus nomenclature for the human ArfGAP domain-containing proteins.

Kahn RA, Bruford E, Inoue H, Logsdon JM, Nie Z, Premont RT, Randazzo PA, Satake M, Theibert AB, Zapp ML, Cassel D - J. Cell Biol. (2008)

Domain organization of human ArfGAP subfamilies and structure of the ArfGAP domain. (A) Representative domain structures of each human ArfGAP subfamily are depicted and are drawn to scale. Abbreviations are: ALPS, ArfGAP1 lipid-packing sensor; ArfGAP, ArfGAP domain; ANK, ankyrin repeat; BAR, Bin/Amphiphysin/Rvs; CALM, CALM binding domain; CB, clathrin-box; CC, coiled-coil; FG repeats, multiple copies of the XXFG motif; GLD, GTP-binding protein-like domain; PBS, Paxillin binding site; PH, pleckstrin homology domain; Pro(PxxP)3, cluster of three Proline-rich (PxxP) motifs; Pro(D/ELPPKP)8, eight tandem Proline-rich (D/ELPPKP) motifs; RA, Ras association motif; RhoGAP, RhoGAP domain; SAM, sterile α-motif; SH3, Src homology 3 domain; SHD, Spa-homology domain. Notes: (1) SMAP2 has CALM BD, but SMAP1 does not. (2) ASAP1 contains the indicated Pro-rich domains; ASAP2 and ASAP3 lack the Pro (D/ELPPKP) repeat and ASAP3 does not have an SH3 domain. (3) AGAP2 has a splice variant with three N-terminal PxxP motifs, called PIKE-L. (B) The structure of the isolated ArfGAP domain of human ArfGAP1 (residues 6–120) is displayed with the backbone shown in green with secondary structures indicated. The side chains of only the conserved arginine (Arg50, on the right) and the four zinc finger cysteines (center; Cys22, 25, 42, and 45) are displayed along with the coordinated Zn2+ (gray sphere). This image was generated using PyMol.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2542466&req=5

fig1: Domain organization of human ArfGAP subfamilies and structure of the ArfGAP domain. (A) Representative domain structures of each human ArfGAP subfamily are depicted and are drawn to scale. Abbreviations are: ALPS, ArfGAP1 lipid-packing sensor; ArfGAP, ArfGAP domain; ANK, ankyrin repeat; BAR, Bin/Amphiphysin/Rvs; CALM, CALM binding domain; CB, clathrin-box; CC, coiled-coil; FG repeats, multiple copies of the XXFG motif; GLD, GTP-binding protein-like domain; PBS, Paxillin binding site; PH, pleckstrin homology domain; Pro(PxxP)3, cluster of three Proline-rich (PxxP) motifs; Pro(D/ELPPKP)8, eight tandem Proline-rich (D/ELPPKP) motifs; RA, Ras association motif; RhoGAP, RhoGAP domain; SAM, sterile α-motif; SH3, Src homology 3 domain; SHD, Spa-homology domain. Notes: (1) SMAP2 has CALM BD, but SMAP1 does not. (2) ASAP1 contains the indicated Pro-rich domains; ASAP2 and ASAP3 lack the Pro (D/ELPPKP) repeat and ASAP3 does not have an SH3 domain. (3) AGAP2 has a splice variant with three N-terminal PxxP motifs, called PIKE-L. (B) The structure of the isolated ArfGAP domain of human ArfGAP1 (residues 6–120) is displayed with the backbone shown in green with secondary structures indicated. The side chains of only the conserved arginine (Arg50, on the right) and the four zinc finger cysteines (center; Cys22, 25, 42, and 45) are displayed along with the coordinated Zn2+ (gray sphere). This image was generated using PyMol.
Mentions: ArfGAPs are a family of proteins containing a characteristic module, the ArfGAP domain, which was first identified in rat ArfGAP1 as the domain responsible for stimulation of GTP hydrolysis on Arf1 (Cukierman et al., 1995). ArfGAP domains are ancient and highly conserved since the earliest eukaryotes. Five ArfGAPs have been identified in the yeast Saccharomyces cerevisiae and shown to display a combination of redundant and unique functions. Mammalian cells express an array of ArfGAPs ranging from relatively small proteins resembling those found in yeast to the large, multi-domain ArfGAPs that are proposed to function as scaffolds for cell signaling (Fig. 1 A).

Bottom Line: At the FASEB summer research conference on "Arf Family GTPases", held in Il Ciocco, Italy in June, 2007, it became evident to researchers that our understanding of the family of Arf GTPase activating proteins (ArfGAPs) has grown exponentially in recent years.Nearly 100 researchers were contacted to generate a consensus nomenclature for human ArfGAPs.This article describes the resulting consensus nomenclature and provides a brief description of each of the 10 subfamilies of 31 human genes encoding proteins containing the ArfGAP domain.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA. rkahn@emory.edu

ABSTRACT
At the FASEB summer research conference on "Arf Family GTPases", held in Il Ciocco, Italy in June, 2007, it became evident to researchers that our understanding of the family of Arf GTPase activating proteins (ArfGAPs) has grown exponentially in recent years. A common nomenclature for these genes and proteins will facilitate discovery of biological functions and possible connections to pathogenesis. Nearly 100 researchers were contacted to generate a consensus nomenclature for human ArfGAPs. This article describes the resulting consensus nomenclature and provides a brief description of each of the 10 subfamilies of 31 human genes encoding proteins containing the ArfGAP domain.

Show MeSH
Related in: MedlinePlus