Protein Family Models

Elongation factor G (EF-G) catalyzes the translocation step of translation. It consists of five structural domains, this entry represents the second domain [1]. This domain adopts a beta barrel structure. This family also includes domains found in other translation factors such as translation initiation factor IF-2, peptide chain release factor, etc. Paper describing PDB structure 1dar. [1]. 8736554. The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange. al-Karadaghi S, Aevarsson A, Garber M, Zheltonosova J, Liljas A;. Structure. 1996;4:555-565. Paper describing PDB structure 1efg. [2]. 8070396. The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution. Czworkowski J, Wang J, Steitz TA, Moore PB;. EMBO J. 1994;13:3661-3668. Paper describing PDB structure 1eft. [3]. 8069622. The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Kjeldgaard M, Nissen P, Thirup S, Nyborg J;. Structure. 1993;1:35-50. Paper describing PDB structure 1fnm. [4]. 11054294. Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site. Laurberg M, Kristensen O, Martemyanov K, Gudkov AT, Nagaev I, Hughes D, Liljas A;. J Mol Biol. 2000;303:593-603. Paper describing PDB structure 1g7r. [5]. 11114334. X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Roll-Mecak A, Cao C, Dever TE, Burley SK;. Cell. 2000;103:781-792. (from Pfam)

Date:

2024-10-16

IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes [1], Bacteria [2] and Archaea [3]). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits [2]. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyses the hydrolysis of GTP following initiation-complex formation [2]. [1]. 17086204. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le. Nature. 2006;444:171-178. [2]. 10878130. Investigation of the translation-initiation factor IF2 gene, infB, as a tool to study the population structure of Streptococcus agalactiae. Hedegaard J, Hauge M, Fage-Larsen J, Mortensen KK, Kilian M, Sperling-Petersen HU, Poulsen K;. Microbiology. 2000;146:1661-1670. [3]. 16169924. Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Falb M, Pfeiffer F, Palm P, Rodewald K, Hickmann V, Tittor J, Oesterhelt D;. Genome Res. 2005;15:1336-1343. (from Pfam)

Date:

2024-10-16

This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase. [1]. 1764105. Tandem translation of E. coli initiation factor IF2 beta: purification and characterization in vitro of two active forms. Nyengaard NR, Mortensen KK, Lassen SF, Hershey JW, Sperling-Petersen HU;. Biochem Biophys Res Commun 1991;181:1572-1579. [2]. 12600987. A conserved structural motif at the N-terminus of bacterial translation initiation factor IF2. Laursen BS, Mortensen KK, Sperling-Petersen HU, Hoffman DW;. 0;0:0-0. (from Pfam)

Date:

2024-10-16

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

Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1]. [1]. 11387043. The Rab GTPase family. Stenmark H, Olkkonen VM;. Genome Biol 2001;2:REVIEWS3007. (from Pfam)

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

translation initiation factor IF-2 protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits; also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex

Date:

2024-04-25

This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initiator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam HMM GTP_EFTU. A shorter form, translated from an alternative start codon more than a hundred codons downstream, is described is IF-2 beta. This model describes the long form, IF-2 alpha.

Gene:

infB

Date:

2024-05-30