Protein Family Models

This domain is found at the C-terminus of tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1]. [1]. 3298234. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR;. J Biol Chem 1987;262:8488-8495. (from Pfam)

Date:

2024-10-16

This family represents a central PRC-barrel domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1]. [1]. 3298234. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR;. J Biol Chem 1987;262:8488-8495. (from Pfam)

Date:

2024-10-16

This family of proteins participate in the biosynthesis of 7-carboxy-7-deazaguanine. They catalyse the conversion of 7-deaza-7-carboxyguanine to preQ0 [1-3]. [1]. 14660578. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. Reader JS, Metzgar D, Schimmel P, de Crecy-Lagard V;. J Biol Chem. 2004;279:6280-6285. [2]. 16199558. Genetic analysis identifies a function for the queC (ybaX) gene product at an initial step in the queuosine biosynthetic pathway in Escherichia coli. Gaur R, Varshney U;. J Bacteriol. 2005;187:6893-6901. [3]. 19354300. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5'-triphosphate in four steps. McCarty RM, Somogyi A, Lin G, Jacobsen NE, Bandarian V;. Biochemistry. 2009;48:3847-3852. [4]. 18491386. Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis. Cicmil N, Huang RH;. Proteins. 2008;72:1084-1088. (from Pfam)

Date:

2024-10-16

This family represents the N-terminal HUP domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1]. [1]. 3298234. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR;. J Biol Chem 1987;262:8488-8495. Paper describing PDB structure 1gpm. [2]. 8548458. The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Tesmer JJ, Klem TJ, Deras ML, Davisson VJ, Smith JL;. Nat Struct Biol 1996;3:74-86. Paper describing PDB structure 2der. [3]. 16871210. Snapshots of tRNA sulphuration via an adenylated intermediate. Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O;. Nature. 2006;442:419-424. Paper describing PDB structure 2vxo. [4]. 23816837. Substrate specificity and oligomerization of human GMP synthetase. Welin M, Lehtio L, Johansson A, Flodin S, Nyman T, Tresaugues L, Hammarstrom M, Graslund S, Nordlund P;. J Mol Biol. 2013;425:4323-4333. Paper describing PDB structure 3vrh. [5]. 23444054. Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA. Nakagawa H, Kuratani M, Goto-Ito S, Ito T, Katsura K, Terada T, Shirouzu M, Sekine S, Shigi N, Yokoyama S;. Proteins. 2013;81:1232-1244. Paper describing PDB structure 5mko. [6]. 28655838. Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster. Arragain S, Bimai O, Legrand P, Caillat S, Ravanat JL, T. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation. [1]. 8895556. Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis. Rizzi M, Nessi C, Mattevi A, Coda A, Bolognesi M, Galizzi A;. EMBO J 1996;15:5125-5134. (from Pfam)

Date:

2024-10-16

This entry represents the N-terminal domain of the Arginosuccinate synthase enzyme. This domain is part of the HUP superfamily. (from Pfam)

Date:

2024-08-14

Most members of this family are asparagine synthase, which catalyzes conversion of aspartate to asparagine. Exceptions that score well against the HMM include isopeptide bond formation proteins for lasso peptide biosynthesis. But note that many additional proteins, such as the 7-cyano-7-deazaguanine synthase QueC, hit with scores barely above the model's cutoff scores to N-terminal regions about 60 amino acids long, whereas the full length of the model is 355.

Date:

2024-08-14