This family represents the N-terminal region of Pescadillo. Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest. This family is often found in conjunction with a pfam00533 domain. Length = 282
>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
HTH_MerR-SF Helix-Turn-Helix DNA binding domain of
80.49
>PF06732 Pescadillo_N: Pescadillo N-terminus; InterPro: IPR010613 Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis
Probab=100.00 E-value=5.3e-45 Score=282.70 Aligned_cols=81 Identities=57% Similarity=0.894 Sum_probs=79.4
Q ss_pred cccccccccchhccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhhcChhHHHhhhc
Q psy14411 5 QKKYEAGEAVRYITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLLHEPNLVIMRQQ 84 (85)
Q Consensus 5 ~kk~~~G~~~~yitR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~hePil~kfRe~ 84 (85)
+|||++|++++||||+||+++|||||+||||||||||||||||++++++|+||++++||||+|||+||+||||+++|||+
T Consensus 1 kkK~~~g~a~~yiTR~qAlkkLQlsl~dFRRLCILKGIyPrePk~k~k~~kg~~~~ktyY~~KDI~~L~hepil~kfRe~ 80 (281)
T PF06732_consen 1 KKKGEKGEAKNYITRNQALKKLQLSLKDFRRLCILKGIYPREPKKKKKVNKGSTAPKTYYHIKDIKFLAHEPILQKFREI 80 (281)
T ss_pred CCCcccccccccccHHHHHHHhcCCHHHHhhHHhhcCccCCCCCcccccccCCCCCceEEEHHHHHHHhccHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred C
Q psy14411 85 R 85 (85)
Q Consensus 85 r 85 (85)
|
T Consensus 81 k 81 (281)
T PF06732_consen 81 K 81 (281)
T ss_pred H
Confidence 5
During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest []. ; GO: 0042254 ribosome biogenesis, 0005730 nucleolus
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment
Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
>TIGR01764 excise DNA binding domain, excisionase family
An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily
Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
