Exoribonuclease superfamilies: structural analysis and phylogenetic distribution - PubMed (original) (raw)

Figure 2

Sequence conservation patterns in the DEDD family. This abbreviated sequence alignment was generated by ClustalX with some editing based on BLAST searches. The focus is on the DEDD RNases, but some DEDD DNases are also listed for comparison. Sequences are from the NCBI non-redundant protein sequence database, unless otherwise stated. Emphasis has been placed on presenting a wide variety of sequences, rather than on completeness due to space limitations. Included are the eight E.coli DEDD family members: EX1_ECOLI, DNA exonuclease I (accession no. G462029); EXOX_ECOLI, DNA exonuclease X (G9789746); DP3E_ECOLI, DNA polymerase III ɛ subunit (G118805); RNT_ECOLI, RNase T (G266952); ORN_ECOLI, oligoribonuclease (G1730261); RND_ECOLI, RNase D (G133152); DPO1_ECOLI, DNA polymerase I (G118825); DPO2_ECOLI, DNA polymerase II (G118829); six S.cerevisiae DEDD RNases: ORN_YEAST, yeast oligoribonuclease (G1730818); REX1_YEAST, yeast RNA exonuclease 1 (G2131716); REX3_YEAST, yeast RNA exonuclease 3 (G6323136); REX4_YEAST, yeast RNA exonuclease 4 (G6324493); PAN2_YEAST, Pan2p subunit of yeast poly(A)-binding protein-dependent poly(A) nuclease (G1709565); RRP6_YEAST, yeast exosome component Rrp6p (G6324574); and proteins from other model organisms: EX1_HAEIN, H.influenzae DNA exonuclease I (G1169569); DP3E_AQUAE, Aquifex aeolicus DNA polymerase III ɛ subunit (G6014995); DPO3_BACSU, B.subtilis DNA polymerase III α chain (G118793); DP3E_HAEIN, H.influenzae DNA polymerase III ɛ subunit (G1169396); RNT_VIBCH, Vibrio cholerae RNase T (G9655469); RNT_BUCSP, Buchnera sp. RNase T (G10038870); RNT_XYLFA, Xylella fastidiosa RNase T (G9107281); RNT_PSEAE, Pseudomonas aeruginosa RNase T (G9949677); RNT_HAEIN, H.influenzae RNase T (G1173107); ORN_HAEIN, H.influenzae oligoribonuclease (G1176352); ORN_MYCTU, Mycobacterium tuberculosis oligoribonuclease (G7227904); ORN_HUMAN, human oligoribonuclease (G7227908); YAA4_SCHPO, S.pombe Pan2p homolog (G1175466); YPO4_CAEEL, C.elegans Pan2p homolog (G1730942); PAN2_DROME, Drosophila melanogaster Pan2p homolog (G7303975); PAN2_HUMAN, human Pan2p homolog (translated from AC023500 with confirmation from ESTs, missing the very C-terminus in G7662258); PARN_HUMAN, human DAN nuclease, a poly(A)-specific 3′ to 5′ exoribonuclease (G4505611); PARN_SCHPO, S.pombe DAN nuclease homolog (G7491557); PARN_CAEEL, C.elegans DAN nuclease homolog (G7505706); RND_HAEIN, H.influenzae RNase D (G1173094); RND_RICPR, Rickettsia prowazekii RNase D (G7467941); RND_MYCTU, M.tuberculosis Rv2681 protein, a RNase D homolog (G7477317); PMC2_HUMAN, human polymyositis-scleroderma overlap syndrome-related nucleolar 100 kDa protein (PM/Scl autoantigen P100) (G8928564); PMC2_DROME, D.melanogaster homolog of PM/Scl autoantigen P100 (G7299933); DPOL_ARCFU, Archaeoglobus fulgidus DNA polymerase (G3122019); DPOD_HUMAN, human DNA polymerase δ catalytic chain (G118839); DPOE_HUMAN, human DNA polymerase ɛ catalytic subunit A (G1352309); EGL_DROME, D.melanogaster egl gene product (G7291631); WRN_HUMAN, human Werner syndrome helicase (G6136393); RND_SYNY3, Synechocystis hypothetical protein (G1001530); RP422_RICPR, R.prowazekii hypothetical protein RP422 (G7467752). The three conserved DEDD motifs are indicated at the top. Highly conserved residues among all family members are highlighted in red. The star at the top marks the fifth highly-conserved acidic residue (highlighted in red) between motifs II and III. Number of residues from the N-termini or residues between conserved blocks are indicated in parentheses. Residues that are highly conserved only within a subfamily are highlighted in blue. Yellow squares highlight some of the characteristic sequence motifs of subfamilies such as two of the three positively-charged, aromatic motifs specific to RNase T proteins, the sequence motif around the fifth conserved acidic residue in oligoribonucleases, and the characteristic motif III of RNase D.