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

Date:

2024-08-14

Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain. [1]. 7491491. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J;. Science 1995;270:1464-1472. (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

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

Stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein

Date:

2021-07-22

This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.

Gene:

prfC

Date:

2024-05-30

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