Protein Family Models for Protein (Select 489190998) - Protein Family Models

Select item 4301221.

Siroheme decarboxylase NirDL-like HTH domain

This entry represents the HTH domains found in siroheme decarboxylase NirdL from Hydrogenobacter thermophilus and related sequences [5]. NirdL is involved in heme d1 biosynthesis. It catalyses the decarboxylation of siroheme into didecarboxysiroheme. Paper describing PDB structure 1i1g. [1]. 11230123. Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. Leonard PM, Smits SH, Sedelnikova SE, Brinkman AB, de Vos WM, van der Oost J, Rice DW, Rafferty JB;. EMBO J. 2001;20:990-997. Paper describing PDB structure 1ri7. [2]. 14976242. The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription. Koike H, Ishijima SA, Clowney L, Suzuki M;. Proc Natl Acad Sci U S A. 2004;101:2840-2845. Paper describing PDB structure 2l4a. [3]. 21338611. The design involved in PapI and Lrp regulation of the pap operon. Kawamura T, Vartanian AS, Zhou H, Dahlquist FW;. J Mol Biol. 2011;409:311-332. Paper describing PDB structure 2zny. [4]. 19004003. Interactions between the archaeal transcription repressor FL11 and its coregulators lysine and arginine. Yamada M, Ishijima SA, Suzuki M;. Proteins. 2009;74:520-525. Paper describing PDB structure 4ch7. [5]. 25083922. The crystal structure of siroheme decarboxylase in complex with iron-uroporphyrin III reveals two essential histidine residues. Haufschildt K, Schmelz S, Kriegler TM, Neumann A, Streif J, Arai H, Heinz DW, Layer G;. J Mol Biol. 2014;426:3272-3286. (from Pfam)

Date:: 2024-10-16

Family Accession:: NF046668.1
Method:: HMM

Select item 4272002.

winged helix-turn-helix transcriptional regulator

Date:: 2024-08-14

Family Accession:: NF024804.5
Method:: HMM

Select item 4236353.

AsnC family transcriptional regulator

GO Terms:

Molecular Function:: sequence-specific DNA binding (GO:0043565)

Date:: 2024-08-14

Family Accession:: NF024796.5
Method:: HMM

Select item 4182084.

HTH domain-containing protein

This family includes helix-turn-helix domains in a wide variety of proteins. (from Pfam)

Date:: 2024-08-14

Family Accession:: NF019884.5
Method:: HMM

Select item 4114295.

Lrp/AsnC ligand binding domain-containing protein

The l-leucine-responsive regulatory protein (Lrp/AsnC) family is a family of similar bacterial transcription regulatory proteins. The family is named after two E. coli proteins involved in regulating amino acid metabolism. This entry corresponds to the usually C-terminal regulatory ligand binding domain. Structurally this domain has a dimeric alpha/beta barrel fold [2]. This domain binds almost exclusively amino acids but also 4-hydroxyphenylpyruvate and kynurenine (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 7770911. The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus. Kyrpides NC, Ouzounis CA;. Trends Biochem Sci 1995;20:140-141. [2]. 17374605. The structure and transcriptional analysis of a global regulator from Neisseria meningitidis. Ren J, Sainsbury S, Combs SE, Capper RG, Jordan PW, Berrow NS, Stammers DK, Saunders NJ, Owens RJ;. J Biol Chem. 2007;282:14655-14664. (from Pfam)

Date:: 2024-10-16

Family Accession:: NF013224.5
Method:: HMM

Select item 4022466.