Protein Family Models

The PEP-CTERM domain is a protein-sorting domain, about 25 amino acids in length, typically found as the most C-terminal domain feature in any bacterial protein. However, a subset of choice-of-anchor J family proteins with PEP-CTERM domains have an additional, extremely unusual novel domain located C-terminally to the PEP-CTERM domain. This domain is found also in proteins that have very little sequence N-terminal to this domain. This HMM represents the first observation of this that has resulting in the naming of a novel domain, and so the domain is named the post-PEP-CTERM-1 domain (PPC1 domain).

Date:

2024-08-14

Ribonuclease J1, as the term is used in Staphylococcus aureus, is one of two RNase J paralogs that are about 40 percent identical.

Gene:

rnjA

Date:

2024-08-03

Ribonuclease J2, as the term is used in Staphylococcus aureus, is one of two RNase J paralogs that are about 40 percent identical. Both

Gene:

rnjB

Date:

2024-08-03

cyclin J family protein similar to human cyclin-J-like protein (CCNJL) that may act as a potential diagnostic biomarker of colon cancer

Date:

2024-02-09

J domain-containing protein similar to the N-terminal conserved domain (called J domain) of DnaJ-like proteins, which is involved in regulating the ATPase activity of heat shock protein 70 (Hsp70) by ATP hydrolysis

Date:

2024-02-09

serine hydrolase domain-containing protein may have hydrolase activity such as Staphylococcus aureus teichoic acid D-alanine hydrolase, transferase activity such as Aspergillus terreus monacolin J acid methylbutanoyltransferase, or may be catalytically inactive

Date:

2024-02-09

photosystem I (PSI) protein PsaX is a component of the cyanobacterial PSI reaction center that is composed of one copy each of PsaA, B, C, D, E, F, I, J, K, L, M and X

Date:

2024-02-09

J domain-containing protein similar to the N-terminal conserved domain (called J domain) of DnaJ-like proteins, which is involved in regulating the ATPase activity of heat shock protein 70 (Hsp70) by ATP hydrolysis

Date:

2024-02-09

J domain-containing protein similar to the N-terminal conserved domain (called J domain) of DnaJ-like proteins, which is involved in regulating the ATPase activity of heat shock protein 70 (Hsp70) by ATP hydrolysis

Date:

2024-02-09

J domain-containing protein containing a similar domain as DnaJ, a protein that plays crucial roles in protein translation, folding, unfolding, translocation, and degradation, primarily by stimulating the ATPase activity of Hsp70.

Date:

2024-02-09

Date:

2024-08-14

This domain represents the polycystin domain from group II of Transient receptor potential (TRP) channels (TRPP) including PKD1, PKD2, PKD2L and mucolipins. The polycystin domain display a sandwich-like shape with five beta-sheets in the tilted middle layer, three alpha-helices on one side and a large loop with two short antiparallel beta-sheets on the other [3]. [1]. 10517637. Polycystin-L is a calcium-regulated cation channel permeable to. calcium ions.. Chen XZ, Vassilev PM, Basora N, Peng JB, Nomura H, Segal Y,. Brown EM, Reeders ST, Hediger MA, Zhou J;. Nature 1999;401:383-386.. [2]. 11264013. Polycystin-2 is a novel cation channel implicated in defective. intracellular Ca(2+) homeostasis in polycystic kidney disease.. Vassilev PM, Guo L, Chen XZ, Segal Y, Peng JB, Basora N,. Babakhanlou H, Cruger G, Kanazirska M, Ye Cp, Brown EM, Hediger. MA, Zhou J;. Biochem Biophys Res Commun 2001;282:341-350.. [3]. 29567962. Cryo-EM structure of the polycystic kidney disease-like channel. PKD2L1.. Su Q, Hu F, Liu Y, Ge X, Mei C, Yu S, Shen A, Zhou Q, Yan C, Lei. J, Zhang Y, Liu X, Wang T;. Nat Commun. 2018;9:1192. (from Pfam)

Date:

2024-08-14

This is the C-terminal domain of Tab2 from plant and cyanobacteria. Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit [1]. Later, the Tab2 homologue from Arabidopsis (Atab2) was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development, presumably functioning as an activator of translation with targets at PSI and PSII [2,3]. Directed mutagenesis experiments carried out in Chlamydomonas reinhardtii, Tab2 Swiss:Q7X8Y6, indicated the importance of a highly conserved C-terminal tripeptide WLL for normal psaB translation [1]. [1]. 14633996. Tab2 is a novel conserved RNA binding protein required for. translation of the chloroplast psaB mRNA.. Dauvillee D, Stampacchia O, Girard-Bascou J, Rochaix JD;. EMBO J. 2003;22:6378-6388.. [2]. 25725436. Large-scale genetic analysis of chloroplast biogenesis in maize.. Belcher S, Williams-Carrier R, Stiffler N, Barkan A;. Biochim Biophys Acta. 2015;1847:1004-1016.. [3]. 17139246. ATAB2 is a novel factor in the signalling pathway of. light-controlled synthesis of photosystem proteins.. Barneche F, Winter V, Crevecoeur M, Rochaix JD;. EMBO J. 2006;25:5907-5918. (from Pfam)

Date:

2024-08-14

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:

2024-08-14

This domain is found towards the C-terminal the U3 small nucleolar RNA-associated protein 20 (UTP20) from yeast and its human homologue, also known as DRIM (Down-Regulated In Metastasis). DRIM is differentially expressed in metastatic and non-metastatic human breast carcinoma cells [1]. Proteins of this entry are involved in processing of non-coding RNA as components of the small-subunit (SSU) processome; SSU processome is involved in the biogenesis of the 18S rRNA [2,3]. UTP20 is a huge alpha-solenoid that functions as a scaffold [4,5]. [1]. 9673349. Differential gene expression in mammary carcinoma cell lines:. identification of DRIM, a new gene down-regulated in metastasis.. Schwirzke M, Gnirke A, Bork P, Tarin D, Weidle UH;. Anticancer Res 1998;18:1409-1421.. [2]. 12837249. A panoramic view of yeast noncoding RNA processing.. Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q,. Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan. OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B,. Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF,. Cell 2003;113:919-933.. [3]. 17498821. Human 1A6/DRIM, the homolog of yeast Utp20, functions in the 18S. rRNA processing.. Wang Y, Liu J, Zhao H, Lu W, Zhao J, Yang L, Li N, Du X, Ke Y;. Biochim Biophys Acta. 2007;1773:863-868.. [4]. 31378463. Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order. of Co-transcriptional 18S rRNA Subdomain Integration.. Cheng J, Bassler J, Fischer P, Lau B, Kellner N, Kunze R,. Griesel S, Kallas M, Berninghausen O, Strauss D, Beckmann R,. Hurt E;. Mol Cell. 2019;75:1256-1269.. [5]. 32943522. Cryo-EM . TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This entry represents a sensor domain consisting of 7 TPR repeats forming a tightly-wound solenoid structure harbouring a deep central pocket. The TPR-S binding pocket is lined with several conserved aromatic and polar residues predicted to bind a NAD+-derived nucleotide in prokaryotic NAD+-derived nucleotide-activated effector conflict systems. It has been acquired at the base of the choanoflagellate-animal lineage as a core component of the ASK signalosome [1]. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic. Immune Systems and Their Diverse Eukaryotic Reformulations.. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam)

Date:

2024-08-14

RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation [1][2]. [1]. 11763972. SPOUT: a class of methyltransferases that includes spoU and trmD. RNA methylase superfamilies, and novel superfamilies of. predicted prokaryotic RNA methylases.. Anantharaman V, Koonin EV, Aravind L;. J Mol Microbiol Biotechnol. 2002;4:71-75.. [2]. 16431987. Identification and characterization of RsmE, the founding member. of a new RNA base methyltransferase family.. Basturea GN, Rudd KE, Deutscher MP;. RNA. 2006;12:426-434. (from Pfam)

Date:

2024-08-14

This entry represents a group of uncharacterised proteins that include methanobactin biosynthesis operon protein MbnP [1]. The respective proteins, MbnP and MbnH, are referred to in the TIGRFAM database as the metallo-mystery pair. [1]. 31511324. MbnH is a diheme MauG-like protein associated with microbial. copper homeostasis.. Kenney GE, Dassama LMK, Manesis AC, Ross MO, Chen S, Hoffman BM,. Rosenzweig AC;. J Biol Chem. 2019;294:16141-16151. (from Pfam)

Date:

2024-08-14

This entry represents the N-terminal domain of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), which is arranged in four supersecondary alpha-helical structures, N1 to N4, that resemble HEAT repeats. Therefore, this domain is also known as N-HEAT. This domain likely mediates DNA binding and, together with the Circular Cradle, forms a ring through which Ku70/80 may present DNA for repair. DNA-PKcs is involved in DNA nonhomologous end joining (NHEJ), required for double-strand break (DSB) repair [1-4]. It is recruited by Ku70/80 heterodimer to DNA ends. [1]. 28154079. DNA-PKcs structure suggests an allosteric mechanism modulating. DNA double-strand break repair.. Sibanda BL, Chirgadze DY, Ascher DB, Blundell TL;. Science. 2017;355:520-524.. [2]. 28652322. Cryo-EM structure of the DNA-PK holoenzyme.. Sharif H, Li Y, Dong Y, Dong L, Wang WL, Mao Y, Wu H;. Proc Natl Acad Sci U S A. 2017;114:7367-7372.. [3]. 28840859. Cryo-EM structure of human DNA-PK holoenzyme.. Yin X, Liu M, Tian Y, Wang J, Xu Y;. Cell Res. 2017;27:1341-1350.. [4]. 33077952. Dimers of DNA-PK create a stage for DNA double-strand break. repair.. Chaplin AK, Hardwick SW, Liang S, Kefala Stavridi A, Hnizda A,. Cooper LR, De Oliveira TM, Chirgadze DY, Blundell TL;. Nat Struct Mol Biol. 2021;28:13-19. (from Pfam)

Date:

2024-08-14

SpoIVA (Sporulation stage IV protein A) acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species [1,2]. This entry represents the C-terminal domain of SpoIVA, which plays a key role in targeting the protein to the outer forespore membrane, in particular the five hydrophobic residues at the extreme C-terminal are essential for this function [1,2]. Structure predictions suggest that it has three conserved alpha helices followed by a beta-hairpin [1]. [1]. 23267091. ATP hydrolysis by a domain related to translation factor GTPases. drives polymerization of a static bacterial morphogenetic. protein.. Castaing JP, Nagy A, Anantharaman V, Aravind L, Ramamurthi KS;. Proc Natl Acad Sci U S A. 2013;110:E151-E160.. [2]. 9922240. A four-dimensional view of assembly of a morphogenetic protein. during sporulation in Bacillus subtilis.. Price KD, Losick R;. J Bacteriol. 1999;181:781-790. (from Pfam)

Date:

2024-08-14