Protein Family Models for Protein (Select 446504626) - Protein Family Models

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Select item 4315491.

Selenocysteine-specific elongation factor, winged helix 1/3

This domain is found twice in Selenocysteine-specific elongation factor from Escherichia coli (SelB) and in similar proteins mainly found in proteobacteria. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. SelB is composed of a N-terminal region, which contains Pfam:PF00009 and Pfam:PF03144, and a C-terminal extension that consists of four winged-helix (WH) domains arranged in tandem. This entry represents the first and third of these motifs, each containing three helices flanked by a three-stranded antiparallel beta-sheet [1]. [1]. 17537456. Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB. Soler N, Fourmy D, Yoshizawa S;. J Mol Biol. 2007;370:728-741. (from Pfam)

Date:: 2024-10-16

Family Accession:: NF045069.2
Method:: HMM

Select item 4287822.

Selenocysteine-specific elongation factor, winged helix domain

This domain is found in Selenocysteine-specific elongation factor from Escherichia coli (SelB) and similar bacterial sequences. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. The C-terminal region of this protein in bacteria shows four winged-helix (WH) domains arranged in tandem, which form two globular structures. This entry represents the second pair of WH domains (WH3 and 4). Each WH domain is an alpha-beta structure consisting of three alpha-helices and a twisted three- stranded antiparallel beta-sheet [1-3]. Paper describing PDB structure 1lva. [1]. 12145214. Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB. Selmer M, Su XD;. EMBO J. 2002;21:4145-4153. Paper describing PDB structure 1wsu. [2]. 15665870. Structural basis for mRNA recognition by elongation factor SelB. Yoshizawa S, Rasubala L, Ose T, Kohda D, Fourmy D, Maenaka K;. Nat Struct Mol Biol. 2005;12:198-203. Paper describing PDB structure 2pjp. [3]. 17537456. Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB. Soler N, Fourmy D, Yoshizawa S;. J Mol Biol. 2007;370:728-741. (from Pfam)

Date:: 2024-10-16

Family Accession:: NF045319.2
Method:: HMM

Select item 4218023.

SelB C-terminal domain-containing protein

Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding [1]. [1]. 12145214. Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB. Selmer M, Su XD;. EMBO J. 2002;21:4145-4153. (from Pfam)

GO Terms:

Biological Process:: selenocysteine incorporation (GO:0001514)

Molecular Function:: RNA binding (GO:0003723)

Molecular Function:: translation elongation factor activity (GO:0003746)

Molecular Function:: GTP binding (GO:0005525)

Cellular Component:: cytoplasm (GO:0005737)

Date:: 2024-10-16

Family Accession:: NF020672.5
Method:: HMM

Select item 4214124.

DNA/RNA-binding winged helix domain-containing protein

GO Terms:

Biological Process:: selenocysteine incorporation (GO:0001514)

Molecular Function:: RNA binding (GO:0003723)

Molecular Function:: translation elongation factor activity (GO:0003746)

Molecular Function:: GTP binding (GO:0005525)

Cellular Component:: cytoplasm (GO:0005737)

Date:: 2024-10-16

Family Accession:: NF020671.5
Method:: HMM

Select item 4142725.

EF-Tu/IF-2/RF-3 family GTPase

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)

GO Terms:

Molecular Function:: GTP binding (GO:0005525)

Date:: 2024-10-16

Family Accession:: NF015126.5
Method:: HMM

Select item 4122036.

GTPase

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).

GO Terms:

Molecular Function:: GTP binding (GO:0005525)

Date:: 2024-10-16

Family Accession:: NF014036.5
Method:: HMM

Select item 4110747.

GTP-binding protein

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)

GO Terms:

Molecular Function:: GTPase activity (GO:0003924)

Molecular Function:: GTP binding (GO:0005525)

Date:: 2024-10-16

Family Accession:: NF012239.5
Method:: HMM

Select item 4083208.