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:

2025-01-31

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:

2025-01-31

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:

2025-02-02

Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions [1]. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent [1]. [1]. 8407793. Characterization of the ferrous iron uptake system of Escherichia coli. Kammler M, Schon C, Hantke K;. J Bacteriol 1993;175:6212-6219. (from Pfam)

Date:

2025-02-02

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:

2025-02-01

Pfam combines a number of different Prosite families together 3D Structure reference. [1]. 7990966. Structure of the human ADP-ribosylation factor 1 complexed with GDP. Amor JC, Harrison DH, Kahn RA, Ringe D;. Nature 1994;372:704-708. Mini review. [2]. 7759471. Structure and function of ARF proteins: Activators of cholera toxin and critical components of intracellular vesicular transport processes. Moss J, Vaughan M;. J. Biol. Chem. 1995;270:12327-12330. [3]. 7770914. Arf proteins: the membrane traffic police?. Boman AL, Kahn RA;. Trends Biochem Sci 1995;20:147-150. [4]. 1899243. Human ADP-ribosylation factors. A functionally conserved family of GTP-binding proteins. Kahn RA, Kern FG, Clark J, Gelmann EP, Rulka C;. J Biol Chem 1991;266:2606-2614. (from Pfam)

Date:

2025-02-01

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:

2025-02-01