Protein Family Models

This entry represents a beta-barrel domain that is found C-terminal in homologues of elongation factor eEF1A. Paper describing PDB structure 1f60. [1]. 11106763. Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha. Andersen GR, Pedersen L, Valente L, Chatterjee I, Kinzy TG, Kjeldgaard M, Nyborg J;. Mol Cell. 2000;6:1261-1266. Paper describing PDB structure 1jny. [2]. 11574461. The crystal structure of Sulfolobus solfataricus elongation factor 1alpha in complex with GDP reveals novel features in nucleotide binding and exchange. Vitagliano L, Masullo M, Sica F, Zagari A, Bocchini V;. EMBO J. 2001;20:5305-5311. Paper describing PDB structure 1r5b. [3]. 15099522. Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe. Kong C, Ito K, Walsh MA, Wada M, Liu Y, Kumar S, Barford D, Nakamura Y, Song H;. Mol Cell. 2004;14:233-245. Paper describing PDB structure 1zun. [4]. 16387658. Molecular basis for G protein control of the prokaryotic ATP sulfurylase. Mougous JD, Lee DH, Hubbard SC, Schelle MW, Vocadlo DJ, Berger JM, Bertozzi CR;. Mol Cell. 2006;21:109-122. Paper describing PDB structure 3e1y. [5]. 19417105. Structural insights into eRF3 and stop codon recognition by eRF1. Cheng Z, Saito K, Pisarev AV, Wada M, Pisareva VP, Pestova TV, Gajda M, Round A, Kong C, Lim M, Nakamura Y, Svergun DI, Ito K, Song H;. Genes Dev. 2009;23:1106-1118. (from Pfam)

Date:

2024-10-29

This HMM identifies the P-loop-containing domain of large numbers of GTPases with ribosome-associated functions, including many involved in ribosome maturation (Der, Era, etc), ribosome rescue (HflX), and protein translation (InfB, Tuf, PrfC).

Date:

2024-10-16

This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. Cryoelectron microscopy structure. [1]. 9311785. Visualization of elongation factor Tu on the Escherichia coli ribosome. Stark H, Rodnina MV, Rinke-Appel J, Brimacombe R, Wintermeyer W, van Heel M;. Nature 1997;389:403-406. (from Pfam)

Date:

2024-10-16

sulfate adenylyltransferase subunit 1 similar to CysN, which acts a regulatory GTPase and is an essential component of the ATP sulfurylase, which catalyzes and couples the energy of GTP hydrolysis to the synthesis of adenosine 5'-phosphosulfate (APS)

Date:

2017-02-03

With CysD catalyzes the formation of adenylylsulfate from sulfate and ATP

Gene:

cysN

Date:

2021-07-23

Metabolic assimilation of sulfur from inorganic sulfate, requires sulfate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulfates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulfation of sulfate with ATP by sulfate adenylyltransferase (ATP sulfurylase) to produce 5'-phosphosulfate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) [1]. In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids [1]. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules [2]. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase) [2,3].

Gene:

cysN

Date:

2021-04-27

Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once. This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.

Date:

2022-03-28