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PROSITE documentation PDOC51710 [for PROSITE entry PS51710]

OBG-type guanine nucleotide-binding (G) domain profile





Description

The P-loop (see <PDOC00017>) guanosine triphosphatases (GTPases) control a multitude of biological processes, ranging from cell division, cell cycling, and signal transduction, to ribosome assembly and protein synthesis. GTPases exert their control by interchanging between an inactive GDP-bound state and an active GTP-bound state, thereby acting as molecular switches. The common denominator of GTPases is the highly conserved guanine nucleotide-binding (G) domain that is responsible for binding and hydrolysis of guanine nucleotides.

Within the translation factor-related (TRAFAC) class of P-loop GTPases, the OBG family comprises a group of high-molecular mass GTPases conserved from bacteria to eukaryotes. The OBG family consists of [1]:

  • Obg from bacteria and eukaryotes [2,3].
  • DRG from eukaryotes and archaea. DRG proteins may regulate fundamental cellular processes through RNA binding [4].
  • Nog1 from eukaryotes and archaea. It is involved in the assembly of the large ribosomal subunit.
  • Yyaf/YchF from bacteria and eukaryotes. It consists of a central G domain, flanked by a coiled-coil domain and a TGS (ThrRS, GTPase, SpoT) domain (see <PDOC51880>). Members of this subfamily bind and hydolyze ATP more efficiently than GTP [5,6].
  • Ygr210 from archaea and fungi.

The OBG-type G domain has a mononucleotide binding fold typical for the P-loop NTPases. A six-stranded mostly parallel β-sheet is flanked by α-helices on both sides (see <PDB:1JAL>). The OBG-type G domain contains five characteristic sequence motifs, termed G1-G5, involved in nucleotide binding and hydrolysis. The G1/Walker A motif (GXXXXGK(S/T)), also referred to as P-loop, helps to position the triphosphate moiety of the bound nucleotide. The G2 (X(T/S)X) and G3/Walker B (hhhDXXG) motifs are involved in the coordination of a Mg(2)+ ion that is required for nucleotide binding and hydrolysis. Specificity in nucleotide binding is conferred by the G4 motif, which has a (N/T)KXD signature in guanine nucleotide binding P-loop NTPases. The G5 motif ((T/G)(C/S)A) supports guanine base recognition [2,3,5,6].

The profile we developed covers the entire OBG-type G domain.

Last update:

March 2014 / First entry.

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Technical section

PROSITE method (with tools and information) covered by this documentation:

G_OBG, PS51710; OBG-type guanine nucleotide-binding (G) domain profile  (MATRIX)


References

1AuthorsLeipe D.D. Wolf Y.I. Koonin E.V. Aravind L.
TitleClassification and evolution of P-loop GTPases and related ATPases.
SourceJ. Mol. Biol. 317:41-72(2002).
PubMed ID11916378
DOI10.1006/jmbi.2001.5378

2AuthorsBuglino J. Shen V. Hakimian P. Lima C.D.
TitleStructural and biochemical analysis of the Obg GTP binding protein.
SourceStructure 10:1581-1592(2002).
PubMed ID12429099

3AuthorsKukimoto-Niino M. Murayama K. Inoue M. Terada T. Tame J.R.H. Kuramitsu S. Shirouzu M. Yokoyama S.
TitleCrystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8.
SourceJ. Mol. Biol. 337:761-770(2004).
PubMed ID15019792
DOI10.1016/j.jmb.2004.01.047

4AuthorsIshikawa K. Azuma S. Ikawa S. Morishita Y. Gohda J. Akiyama T. Semba K. Inoue J.i.
TitleCloning and characterization of Xenopus laevis drg2, a member of the developmentally regulated GTP-binding protein subfamily.
SourceGene 322:105-112(2003).
PubMed ID14644502

5AuthorsTeplyakov A. Obmolova G. Chu S.Y. Toedt J. Eisenstein E. Howard A.J. Gilliland G.L.
TitleCrystal structure of the YchF protein reveals binding sites for GTP and nucleic acid.
SourceJ. Bacteriol. 185:4031-4037(2003).
PubMed ID12837776

6AuthorsKoller-Eichhorn R. Marquardt T. Gail R. Wittinghofer A. Kostrewa D. Kutay U. Kambach C.
TitleHuman OLA1 defines an ATPase subfamily in the Obg family of GTP-binding proteins.
SourceJ. Biol. Chem. 282:19928-19937(2007).
PubMed ID17430889
DOI10.1074/jbc.M700541200



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