Protein Family Models

frizzled family protein similar to the ten frizzleds (Fzd1-10) and smoothened (Smo), which are involved in transmitting the signals of Wnts and hedgehog proteins and are seven transmembrane-spanning proteins that constitute an unconventional class of G protein-coupled receptors; contains an N-terminal extracellular cysteine-rich domain (CRD) associated with their role in binding to Wnt ligands

Date:

2023-10-31

REF is a family of P1-like phage RecA-dependent nucleases. It does not appear to act as a positive RecA regulator. It is a new kind of enzyme, a RecA-dependent nuclease [1]. [1]. 21193392. Creating directed double-strand breaks with the Ref protein: a. novel RecA-dependent nuclease from bacteriophage P1.. Gruenig MC, Lu D, Won SJ, Dulberger CL, Manlick AJ, Keck JL, Cox. MM;. J Biol Chem. 2011;286:8240-8251. (from Pfam)

Date:

2024-04-03

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001589) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the exopolysaccharides biosynthetic gene cluster from Burkholderia cenocepacia J2315 [1]. This family appears to be predominantly found in Proteobacteria. [1]. 28658258. Genome-scale analysis of the genes that contribute to. Burkholderia pseudomallei biofilm formation identifies a crucial. exopolysaccharide biosynthesis gene cluster.. Borlee GI, Plumley BA, Martin KH, Somprasong N, Mangalea MR,. Islam MN, Burtnick MN, Brett PJ, Steinmetz I, AuCoin DP, Belisle. JT, Crick DC, Schweizer HP, Borlee BR;. PLoS Negl Trop Dis. 2017;11:e0005689. (from Pfam)

Date:

2024-04-03

Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI) (Pfam:PF01688), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation [1]. This entry represents the N-terminal domain of gE, which interacts with gI [2,3]. [1]. 10881679. Epitopes on glycoprotein E and on the glycoprotein. E/glycoprotein I complex of bovine herpesvirus 1 are expressed. by all of 222 isolates and 11 vaccine strains.. Rijsewijk FA, Kaashoek MJ, Langeveld JP, Maris-Veldhuis MA,. Magdalena J, Verschuren SB, Meloen RH, van Oirschot JT;. Arch Virol 2000;145:921-936.. [2]. 16646632. Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a. mechanism for antibody bipolar bridging.. Sprague ER, Wang C, Baker D, Bjorkman PJ;. PLoS Biol. 2006;4:e148.. [3]. 11689673. An N-terminal domain of herpes simplex virus type Ig E is. capable of forming stable complexes with gI.. Rizvi SM, Raghavan M;. J Virol. 2001;75:11897-11901. (from Pfam)

Date:

2024-04-03

CTC1 is one of the three components of the CST complex that assists Shelterin to protect the ends of telomeres from attack by DNA-repair mechanisms. Mutations in human CTC1 have been recognised as contributing to cerebroretinal microangiopathy. [1]. 19854130. RPA-like mammalian Ctc1-Stn1-Ten1 complex binds to. single-stranded DNA and protects telomeres independently of the. Pot1 pathway.. Miyake Y, Nakamura M, Nabetani A, Shimamura S, Tamura M,. Yonehara S, Saito M, Ishikawa F;. Mol Cell. 2009;36:193-206.. [2]. 22267198. Mutations in CTC1, encoding conserved telomere maintenance. component 1, cause Coats plus.. Anderson BH, Kasher PR, Mayer J, Szynkiewicz M, Jenkinson EM,. Bhaskar SS, Urquhart JE, Daly SB, Dickerson JE, O'Sullivan J,. Leibundgut EO, Muter J, Abdel-Salem GM, Babul-Hirji R, Baxter P,. Berger A, Bonafe L, Brunstom-Hernandez JE, Buckard JA, Chitayat. D, Chong WK, Cordelli DM, Ferreira P, Fluss J, Forrest EH,. Franzoni E, Garone C, Hammans SR, Houge G, Hughes I, Jacquemont. S, Jeannet PY, Jefferson RJ, Kumar R, Kutschke G, Lundberg S,. Lourenco CM, Mehta R, Naidu S, Nischal KK, Nunes L, Ounap K,. Philippart M, Prabhakar P, Risen SR, Schiffmann R, Soh C,. Stephenson JB, Stewart H, Stone J, Tolmie JL, van der Knaap MS,. Vieira JP, Vilain CN, Wakeling EL, Wermenbol V, Whitney A,. Lovell SC, Meyer S, Livingston JH, Baerlocher GM, Black GC, Rice. GI, Crow YJ;. Nat Genet. 2012;44:338-342.. [3]. 22387016. Mutations in CTC1, encoding the CTS telomere maintenance complex. component 1, cause cerebroretinal microangiopathy with. calcifications and cysts.. Polvi A, Linnankivi T, Kivela T, Herva R, Keating JP, Makitie O,. P. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-04-03

HHV-1_VABD is the short region of the Herpes simplex 1 virus' specific signature adaptor protein that binds to the cellular mRNA export factor such as mouse REF [1]. [1]. 21253573. Structural basis for the recognition of cellular mRNA export. factor REF by herpes viral proteins HSV-1 ICP27 and HVS ORF57.. Tunnicliffe RB, Hautbergue GM, Kalra P, Jackson BR, Whitehouse. A, Wilson SA, Golovanov AP;. PLoS Pathog. 2011;7:e1001244. (from Pfam)

Date:

2024-04-03

The plant specific protein family, which comprises EDS1 (Enhanced disease susceptibility 1), PAD4 (Phytoalexin deficient4) and SAG101 (Senescence-associated gene 101), is involved in innate immunity [Ref.1]. Signaling by intracellular immune receptors with NB-ARC domain (Pfam:PF00931) relies on this protein family [1,3]. C-terminus of Arabidopsis EDS1 and PAD4 proteins did not have recognizable sequence homology to other domains and therefore named EP domain (EDS1-PAD4) [2]. A combination of an N-terminal lipase_3 domain (Pfam:PF01764) and the C-terminal EP-domain is the defining feature of this family. Structurally, EP domain comprises exclusively of alpha-helices (PDB:4NFU) [1]. Structure-function analysis of Arabidopsis proteins showed that EDS1 forms heterodimers with PAD4 or SAG101, chiefly through the N-terminal lipase_3 domain. These heterodimers are essential for plant defense signaling. The EP domain is not stable without the lipase_3 domain, but is required for immunity [1]. Mutations of conserved residues in the EP domain of EDS1 strongly affect its immune signaling function [4]. [1]. 24331460. Structural basis for signaling by exclusive EDS1 heteromeric. complexes with SAG101 or PAD4 in plant innate immunity.. Wagner S, Stuttmann J, Rietz S, Guerois R, Brunstein E, Bautor. J, Niefind K, Parker JE;. Cell Host Microbe. 2013;14:619-630.. [2]. 11574472. Direct interaction between the Arabidopsis disease resistance. signaling proteins, EDS1 and PAD4.. Feys BJ, Moisan LJ, Newman MA, Parker JE;. EMBO J. 2001;20:5400-5411.. [3]. 9707643. Different requirements for EDS1 and NDR1 by disease resistance. genes define at le. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-04-03

This entry corresponds to a bacteriocin from the bacterium Brevibacillus laterosporus called laterosporulin. This peptide has a defensin-like structure [2]. [1]. 22403615. Identification, purification and characterization of. laterosporulin, a novel bacteriocin produced by Brevibacillus. sp. strain GI-9.. Singh PK, Chittpurna, Ashish, Sharma V, Patil PB, Korpole S;. PLoS One. 2012;7:e31498.. [2]. 25345978. The intramolecular disulfide-stapled structure of. laterosporulin, a class IId bacteriocin, conceals a human. defensin-like structural module.. Singh PK, Solanki V, Sharma S, Thakur KG, Krishnan B, Korpole S;. FEBS J. 2015;282:203-214. (from Pfam)

Date:

2024-04-03

The 3cjl structure is likely a representative of a new fold with some resemblance to 3-helical bundle folds such as the serum albumin-like fold of SCOP. No significant hits reported by a Dali search. This protein is the first structural representative of a small (about 60 proteins) family of proteins that are found among proteo- and enterobacteria (REF http://www.topsan.org/Proteins/JCSG/3CJL). (from Pfam)

Date:

2023-12-12

Family based of PDB:3B5P encoded by ZP_00108531 from nitrogen-fixing cyanobacterium Nostoc punctiforme pcc 73102 is a CADD-like protein of unknown function. Superposition between protein structures encoded by CT610 from Chlamydia trachomatis (PDB code 1rwc), pyrroloquinolinquinone synthase C (PqqC, PDB code 1otv) and ZP_00108531 revealed that putative active sites in CT610 and ZP_00108531 are identical. ( REF: http://www.topsan.org/Proteins/JCSG/3B5P). (from Pfam)

Date:

2023-12-12

This domain is found in the N-terminal region of Gcn1 protein, which acts as a translation activator that mediates translational control by regulating Gcn2 kinase activity [1]. [1]. 11350982. Budding yeast GCN1 binds the GI domain to activate the eIF2alpha. kinase GCN2.. Kubota H, Ota K, Sakaki Y, Ito T;. J Biol Chem. 2001;276:17591-17596. (from Pfam)

Date:

2024-04-03

PDB:3D4E shared structural similarity to beta-lactamase inhibitory proteins (BLIP) which already include 1XXM, 1S0W, 1JTG, 2G2U, 2G2W, 2B5R, and 3due. All of structures are involved in beta-lactamase inhibitor complex. (REF http://www.topsan.org/Proteins/JCSG/3d4e) (from Pfam)

Date:

2023-12-12

This domain is an ADP-ribose binding module. It is found in a number of yeast proteins. [1]. 10550052. A biochemical genomics approach for identifying genes by the. activity of their products.. Martzen MR, McCraith SM, Spinelli SL, Torres FM, Fields S,. Grayhack EJ, Phizicky EM;. Science 1999;286:1153-1155.. [2]. 15902274. The macro domain is an ADP-ribose binding module.. Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait. F, Bycroft M, Ladurner AG;. EMBO J 2005;24:1911-1920.. [3]. 19273270. Sensing NAD metabolites through macro domains.. Till S, Ladurner AG;. Front Biosci. 2009;14:3246-3258. (from Pfam)

Date:

2024-04-03

The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats [1]. In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex [2]. [1]. 9707445. A novel yeast gene, THO2, is involved in RNA pol II. transcription and provides new evidence for transcriptional. elongation-associated recombination.. Piruat JI, Aguilera A;. EMBO J. 1998;17:4859-4872.. [2]. 17095540. Protein composition of human mRNPs spliced in vitro and. differential requirements for mRNP protein recruitment.. Merz C, Urlaub H, Will CL, Luhrmann R;. RNA. 2007;13:116-128. (from Pfam)

Date:

2024-04-03

The membrane bound F1-FO-type H+ ATP synthase of mitochondria catalyses the terminal step in oxidative respiration converting the generation of the electrochemical gradient into ATP for cellular biosynthesis. The general structure and the core subunits of the enzyme are highly conserved in both prokaryotic and eukaryotic organisms. [1]. 8702768. Membrane topography and near-neighbor relationships of the. mitochondrial ATP synthase subunits e, f, and g.. Belogrudov GI, Tomich JM, Hatefi Y;. J Biol Chem. 1996;271:20340-20345.. [2]. 12681508. The products of the mitochondrial orf25 and orfB genes are FO. components in the plant F1FO ATP synthase.. Heazlewood JL, Whelan J, Millar AH;. FEBS Lett. 2003;540:201-205. (from Pfam)

Date:

2024-04-03

This proteins is the product of the gene MPN330 and is thought to involved in a cellular function that has yet to be characterised. The proteins has 11 helices and a novel fold [1]. No function is currently known for this protein. [1]. 15562512. Crystal structure of the conserved hypothetical protein MPN330. (GI: 1674200) from Mycoplasma pneumoniae.. Das D, Oganesyan N, Yokota H, Pufan R, Kim R, Kim SH;. Proteins. 2005;58:504-508. (from Pfam)

Date:

2024-04-03

Mastoparans are a family of tetradecapeptides from wasp venom, that have been shown to directly activate GTP-binding regulatory proteins. These peptides show selectivity among G proteins: they strongly activate Go and Gi but not Gs or Gt. The peptide of this family are composed by 14 amino acids but they can assume different structures [1]. [1]. 9537994. G protein-bound conformation of mastoparan-X: heteronuclear. multidimensional transferred nuclear overhauser effect analysis. of peptide uniformly enriched with 13C and 15N.. Kusunoki H, Wakamatsu K, Sato K, Miyazawa T, Kohno T;. Biochemistry 1998;37:4782-4790. (from Pfam)

Date:

2024-04-03

Coq4p was shown to peripherally associate with the matrix face of the mitochondrial inner membrane. The putative mitochondrial- targeting sequence present at the amino-terminus of the polypeptide efficiently imported it to mitochondria. The function of Coq4p is unknown, although its presence is required to maintain a steady-state level of Coq7p, another component of the Q biosynthetic pathway [1]. The overall structure of Coq4 is alpha helical and shows resemblance to haemoglobin/myoglobin (information from TOPSAN). [1]. 11469793. Yeast COQ4 encodes a mitochondrial protein required for coenzyme. Q synthesis.. Belogrudov GI, Lee PT, Jonassen T, Hsu AY, Gin P, Clarke CF;. Arch Biochem Biophys 2001;392:48-58. (from Pfam)

Date:

2024-04-03

This family consists of several circumsporozoite-related antigen (CRA) or exported protein-1 (EXP1) sequences found specifically in Plasmodium species. The function of this family is unknown. [1]. 8050527. Plasmodium falciparum: exported protein-1, a blood stage. antigen, is expressed in liver stage parasites.. Sanchez GI, Rogers WO, Mellouk S, Hoffman SL;. Exp Parasitol 1994;79:59-62. (from Pfam)

Date:

2024-04-03

Transposase_21 proteins are present mostly in plants, with members horizontally transferred to Bifidobacterium breve (GI: 291457831). Both DUF1258 Pfam:PF06869 and Transposase_21 have conserved active site residues similar to RNase H-like proteins, which suggests that they are functional transposases (1). [1]. 24464998. The RNase H-like superfamily: new members, comparative. structural analysis and evolutionary classification.. Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A,. Nowotny M, Ginalski K, Bujnicki JM;. Nucleic Acids Res. 2014;42:4160-4179. (from Pfam)

Date:

2024-04-03