Protein Family Models

The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain [1-2]. [1]. 12730230. The GTPase activity and C-terminal cysteine of the Escherichia. coli MnmE protein are essential for its tRNA modifying function.. Yim L, Martinez-Vicente M, Villarroya M, Aguado C, Knecht E,. Armengod ME;. J Biol Chem. 2003;278:28378-28387.. [2]. 19806182. Kissing G domains of MnmE monitored by X-ray crystallography and. pulse electron paramagnetic resonance spectroscopy.. Meyer S, Bohme S, Kruger A, Steinhoff HJ, Klare JP, Wittinghofer. A;. PLoS Biol. 2009;7:e1000212. (from Pfam)

Date:

2024-08-14

This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP. TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein [1]. [1]. 15616586. The structure of the TrmE GTP-binding protein and its. implications for tRNA modification.. Scrima A, Vetter IR, Armengod ME, Wittinghofer A;. EMBO J. 2005;24:23-33. (from Pfam)

Date:

2024-08-14

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:

2024-08-14

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:

2024-08-14

Gene:

mnmE

Date:

2021-07-23

tRNA modification GTPase is involved in the modification of the wobble position of certain tRNAs and is one of the G proteins activated by nucleotide-dependent dimerization, such as bacterial MnmE and mitochondrial GTP-binding protein 3

Date:

2024-09-09

MnmE, previously known as ThdF (thiophene and furan oxidation protein) and TrmE, is a GTPase involved in tRNA modification to create 5-met hylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and MnmG (previously GidA) form an alpha2/beta2 heterotetramer.

Gene:

mnmE

Date:

2021-07-23

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