Protein Family Models

This family includes Cat eye syndrome critical region protein 6, a protein which has been identified in a screen for candidate genes for the developmental disorder Cat Eye Syndrome (CES) [1]. It also includes the TMEM121 transmembrane proteins. The function of this family is unknown. [1]. 11381032. Analysis of the cat eye syndrome critical region in humans and. the region of conserved synteny in mice: a search for candidate. genes at or near the human chromosome 22 pericentromere.. Footz TK, Brinkman-Mills P, Banting GS, Maier SA, Riazi MA,. Bridgland L, Hu S, Birren B, Minoshima S, Shimizu N, Pan H,. Nguyen T, Fang F, Fu Y, Ray L, Wu H, Shaull S, Phan S, Yao Z,. Chen F, Huan A, Hu P, Wang Q, Loh P, Qi S, Roe BA, McDermid HE;. Genome Res. 2001;11:1053-1070. (from Pfam)

Date:

2024-08-14

This entry represents the C-terminal region of protein Inscuteable (Insc) containing four putative armadillo repeats and the conserved extreme C-terminal tetrapeptide Glu-Ser-Phe-Val which is in agreement with the class I PDZ-binding motif X-Ser/Thr-X-/ (X and /are unspecified and hydrophobic residues, respectively). Insc functions as an adaptor protein that binds simultaneously with Partner of Insc (Pins, consisting of alpha subunit (Ga) of heterotrimeric G proteins and its guanine nucleotide dissociation inhibitor) and Par3 (PDZ-containing proteins) to regulate their apical localisation in neuroblasts, which is required for the correct execution of the asymmetric division [1,2]. [1]. 16458856. Two forms of human Inscuteable-related protein that links Par3. to the Pins homologues LGN and AGS3.. Izaki T, Kamakura S, Kohjima M, Sumimoto H;. Biochem Biophys Res Commun. 2006;341:1001-1006.. [2]. 21816348. LGN/mInsc and LGN/NuMA complex structures suggest distinct. functions in asymmetric cell division for the Par3/mInsc/LGN and. Galphai/LGN/NuMA pathways.. Zhu J, Wen W, Zheng Z, Shang Y, Wei Z, Xiao Z, Pan Z, Du Q, Wang. W, Zhang M;. Mol Cell. 2011;43:418-431. (from Pfam)

Date:

2024-08-14

This domain is found in calcium-binding and coiled-coil domain 2/NDP25 (CALCOCO2/NDP25) found in Homo sapiens. CALCOCO2/NDP25 is an ubiquitin-binding autophagy receptor involved in the selective autophagic degradation of invading pathogens. This domain is a typical C2H2-type zinc finger which specifically recognizes mono-ubiquitin or poly-ubiquitin chain. The overall ubiquitin-binding mode utilizes the C-terminal alpha-helix to interact with the solvent-exposed surface of the central beta-sheet of ubiquitin, similar to that observed in the RABGEF1/Rabex-5 or POLN/Pol-eta zinc finger [1]. [1]. 26506893. Molecular basis of ubiquitin recognition by the autophagy. receptor CALCOCO2.. Xie X, Li F, Wang Y, Wang Y, Lin Z, Cheng X, Liu J, Chen C, Pan. L;. Autophagy. 2015;11:1775-1789. (from Pfam)

Date:

2024-08-14

HGAL is a family of mammalian sequences typically between 104 and 179 amino acids in length. Members were discovered in a search for proteins precipitating diffuse large B-cell lymphomas [1,2]. HGAL interacts with the cytoskeleton and aids the activity of interleukin-6 on cell migration [3]. It also modulates the RhoA signalling pathway [4]. [1]. 12509382. HGAL is a novel interleukin-4-inducible gene that strongly. predicts survival in diffuse large B-cell lymphoma.. Lossos IS, Alizadeh AA, Rajapaksa R, Tibshirani R, Levy R;. Blood. 2003;101:433-440.. [2]. 12819018. Two newly characterized germinal center B-cell-associated genes,. GCET1 and GCET2, have differential expression in normal and. neoplastic B cells.. Pan Z, Shen Y, Du C, Zhou G, Rosenwald A, Staudt LM, Greiner TC,. McKeithan TW, Chan WC;. Am J Pathol. 2003;163:135-144.. [3]. 17823310. HGAL, a lymphoma prognostic biomarker, interacts with the. cytoskeleton and mediates the effects of IL-6 on cell migration.. Lu X, Chen J, Malumbres R, Cubedo Gil E, Helfman DM, Lossos IS;. Blood. 2007;110:4268-4277.. [4]. 20844236. HGAL, a germinal center specific protein, decreases lymphoma. cell motility by modulation of the RhoA signaling pathway.. Jiang X, Lu X, McNamara G, Liu X, Cubedo E, Sarosiek KA,. Sanchez-Garcia I, Helfman DM, Lossos IS;. Blood. 2010;116:5217-5227. (from Pfam)

Date:

2024-08-14

Interactions with ankyrin-G are crucial to the localisation of voltage-gated sodium channels (VGSCs) at the axon initial segment and for neurons to initiate action potentials. This conserved 9-amino acid motif ((V/A)P(I/L)AXXE(S/D)D) is required for ankyrin-G binding and functions to localise sodium channels to a variety of 'excitable' membrane domains both inside and outside of the nervous system [1]. This motif has also been identified in the potassium channel 6TM proteins KCNQ2 and KCNQ3 [2], that correspond to the M channels that exert a crucial influence over neuronal excitability. KCNQ2/KCNQ3 channels are preferentially localised to the surface of axons both at the axonal initial segment and more distally, and this axonal initial segment targeting of surface KCNQ channels is mediated by these ankyrin-G binding motifs of KCNQ2 and KCNQ3 [3]. KCNQ3 is a major determinant of M channel localisation to the AIS, rather than KCNQ2 [4]. Phylogenetic analysis reveals that anchor motifs evolved sequentially in chordates (NaV channel) and jawed vertebrates (KCNQ2/3) [5]. [1]. 12716895. Identification of a conserved ankyrin-binding motif in the. family of sodium channel alpha subunits.. Lemaillet G, Walker B, Lambert S;. J Biol Chem. 2003;278:27333-27339.. [2]. 16525039. A common ankyrin-G-based mechanism retains KCNQ and NaV channels. at electrically active domains of the axon.. Pan Z, Kao T, Horvath Z, Lemos J, Sul JY, Cranstoun SD, Bennett. V, Scherer SS, Cooper EC;. J Neurosci. 2006;26:2599-2613.. [3]. 16735477. Polarized axonal surface expression of neuronal KCNQ channels is. mediated by multiple signals in the KCNQ2 and KC. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

Members of this family of sugar isomerases belong to the cupin superfamily and consist of group I and II of D-lyxose isomerases [3]. The enzyme from Cohnella laevoribosii has been shown to be specific for D-lyxose, L-ribose, and D-mannose [1]. E. coli sugar isomerase (EcSI) shows a preference for D-lyxose and D-mannose [2] and its active site is highly similar to YdaE from the sigma B regulon of Bacillus subtilis [3]. [1]. 17189362. Characterization of a novel D-lyxose isomerase from Cohnella. laevoribosii RI-39 sp. nov.. Cho EA, Lee DW, Cha YH, Lee SJ, Jung HC, Pan JG, Pyun YR;. J Bacteriol. 2007;189:1655-1663.. [2]. 20615418. Structure-based annotation of a novel sugar isomerase from the. pathogenic E. coli O157:H7.. van Staalduinen LM, Park CS, Yeom SJ, Adams-Cioaba MA, Oh DK,. Jia Z;. J Mol Biol. 2010;401:866-881.. [3]. 34422783. Biochemical and Structural Characterisation of a Novel D-Lyxose. Isomerase From the Hyperthermophilic Archaeon Thermofilum sp.. De Rose SA, Kuprat T, Isupov MN, Reinhardt A, Schonheit P,. Littlechild JA;. Front Bioeng Biotechnol. 2021;9:711487.. [4]. 21520290. The structure of a D-lyxose isomerase from the sigmaB regulon of. Bacillus subtilis.. Marles-Wright J, Lewis RJ;. Proteins. 2011;79:2015-2019. (from Pfam)

Date:

2024-08-14

TRIC (trimeric intracellular cation) channels are differentially expressed in intracellular stores in animal cell types. TRIC subtypes contain three proposed transmembrane segments, and form homo-trimers with a bullet-like structure. Electrophysiological measurements with purified TRIC preparations identify a monovalent cation-selective channel [1]. [1]. 17611541. TRIC channels are essential for Ca2+ handling in intracellular. stores.. Yazawa M, Ferrante C, Feng J, Mio K, Ogura T, Zhang M, Lin PH,. Pan Z, Komazaki S, Kato K, Nishi M, Zhao X, Weisleder N, Sato C,. Ma J, Takeshima H;. Nature. 2007;448:78-82. (from Pfam)

Date:

2024-08-14

Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. This family includes members such as LPTD found in Shigella flexneri and Yersinia pestis. Structural analysis indicates that LptD forms a novel 26-stranded beta-barrel. It interacts with LPTE where LptE adopts a roll-like structure located inside the barrel of LptD. The LPS translocon LptD is unable to fold properly in the absence of LptE and the two proteins form a unique barrel and plug architecture for LPS transport and insertion [1] [2]. LptD is an essential outer membrane protein that mediates the final transport of lipopolysaccharide (LPS) to outer leaflet. It has been suggested that LptD is a promising target for the development of effective vaccines and antibody-based therapies to control Vibrio infection [3]. [1]. 24990744. Structural basis for outer membrane lipopolysaccharide. insertion.. Dong H, Xiang Q, Gu Y, Wang Z, Paterson NG, Stansfeld PJ, He C,. Zhang Y, Wang W, Dong C;. Nature. 2014;511:52-56.. [2]. 27161977. Structural and Functional Characterization of the LPS. Transporter LptDE from Gram-Negative Pathogens.. Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K,. Wojtowicz D, Barnard TJ, Gumbart JC, Buchanan SK;. Structure. 2016;24:965-976.. [3]. 27922123. LptD is a promising vaccine antigen and potential. immunotherapeutic target for protection against Vibrio species. infection.. Zha Z, Li C, Li W, Ye Z, Pan J;. Sci Rep. 2016;6:38577. (from Pfam)

Gene:

lptD

Date:

2024-08-14

YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs [2,3,4]. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices [5]. [1]. 15965736. NMR solution structure of Thermotoga maritima protein TM1509. reveals a Zn-metalloprotease-like tertiary structure.. Penhoat CH, Li Z, Atreya HS, Kim S, Yee A, Xiao R, Murray D,. Arrowsmith CH, Szyperski T;. J Struct Funct Genomics. 2005;6:51-62.. [2]. 23273979. Conserved bacterial RNase YbeY plays key roles in 70S ribosome. quality control and 16S rRNA maturation.. Jacob AI, Kohrer C, Davies BW, RajBhandary UL, Walker GC;. Mol Cell. 2013;49:427-438.. [3]. 20807199. Role of Escherichia coli YbeY, a highly conserved protein, in. rRNA processing.. Davies BW, Kohrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM,. Rajbhandary UL, Walker GC;. Mol Microbiol. 2010;78:506-518.. [4]. 32605982. Endoribonuclease YbeY Is Essential for RNA Processing and. Virulence in Pseudomonas aeruginosa.. Xia Y, Weng Y, Xu C, Wang D, Pan X, Tian Z, Xia B, Li H, Chen R,. Liu C, Ji. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin. [1]. 3102969. Structure of co-crystals of tropomyosin and troponin.. White SP, Cohen C, Phillips GN Jr;. Nature 1987;325:826-828.. [2]. 7852318. A direct regulatory role for troponin T and a dual role for. troponin C in the Ca2+ regulation of muscle contraction.. Potter JD, Sheng Z, Pan BS, Zhao J;. J Biol Chem 1995;270:2557-2562.. [3]. 7601340. The troponin complex and regulation of muscle contraction.. Farah CS, Reinach FC;. FASEB J 1995;9:755-767. (from Pfam)

Date:

2024-08-14