Protein Family Models

ribosome biogenesis GTPase Der (EngA) is an essential bacterial GTPase that is required for 50S ribosomal subunit stability; it contains two consecutive GTPase domains and a KH-domain

Date:

2024-11-05

The KH-like domain at the C-terminus of the EngA subfamily of essential bacterial GTPases has a unique domain structure position. The two adjacent GTPase domains (GD1 and GD2), two domains of family MMR_HSR1, Pfam:PF01926, pack at either side of the C-terminal domain. This C-terminal domain resembles a KH domain but is missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2. This family has not been added to the KH clan since SCOP classifies it separately due to its missing the key KH motif/fold. [1]. 12467572. Domain arrangement of Der, a switch protein containing two GTPase domains. Robinson VL, Hwang J, Fox E, Inouye M, Stock AM;. Structure. 2002;10:1649-1658. (from Pfam)

Date:

2024-10-16

Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria. [1]. 8742710. Isolation of Arabidopsis genes that differentiate between resistance responses mediated by the RPS2 and RPM1 disease resistance genes. Reuber TL, Ausubel FM;. Plant Cell 1996;8:241-249. (from Pfam)

Date:

2024-10-16

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:

2024-10-16

This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif [2,3]. HypB has GTPase activity and is a guanine nucleotide binding protein [3]. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression [1]. UreG is required for functional incorporation of the urease nickel metallocenter.[4] GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins [1]. This family of domains also contains P47K (Swiss:P31521), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product (Swiss:P29937), which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans [5]. [1]. 9140970. The HypB protein from Bradyrhizobium japonicum can store nickel and is required for the nickel-dependent transcriptional regulation of hydrogenase. Olson JW, Fu C, Maier RJ;. Mol Microbiol 1997;24:119-128. [2]. 9209019. Characterization of UreG, identification of a UreD-UreF-UreG complex, and evidence suggesting that a nucleotide-binding site in UreG is required for in vivo metallocenter assembly of Klebsiella aerogenes urease. Moncrief MB, Hausinger RP;. J Bacteriol 1997;179:4081-4086. [3]. 8423137. The product of the hypB gene, which is required for nickel incorporation into hydrogenases, is a novel guanine nucleotide-binding protein. Maier T, Jacobi A, Sauter M, Bock A;. J Bacteriol 1993;175:630-635. [4]. 1624427. Klebsi. TRUNCATED at 1650 bytes (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

EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.

Gene:

der

Date:

2021-04-27