Analysis of the proteins responsible for The DNA degradation (Dnd) system

DndA DndB DndC DndD DndE
Dnd protein DndD
Putative function Putative ATPase with DNA nicking activity, may couple ATP hydrolysis to DndE function
DndD sequence of Streptomyces lividans 1326 MNGCGKTTLLDAIQLVLYGPRARCSGRGNRSYDTYLRESINRAADPQRGAELRLEFSITVEGRPRTYEVARTWFAKGKQV
RESLAVTVDGKYDDTISETWAEHVEEILPLEVASLFFFDGEKVEQLADPERAADVIEAAVQSLLGVRAVEQLRTDLLALQ
RRQRLSQEDQGILEQIRDLKVKSQAAAQEVSDQSQLLAQATSHLDVAQAQLAKIERDFERAGGRLYEERRGLEAAKEATA
ERLAQTQKDLRGLAEGPLPLLLLRGELAALQEQSVREQEAAEARQVIGVLERRDAWLVDQLPDGVPAADRTALKRKLTAD
RKKRAAATELALDLSLPPDLPQKLAALDEVLETDAARAAELLRSADKTVHELQQAERQLAAVPDEQQIKTLIEDRQQASE
AVIVARAAVEQHRELVAEARSRHERLEADLERARQKMVRTFVREEELQRVVAYADKARTTLDRFGEALLRKHISSLEVAV
LRSFQTLMRKSGLIKDLRIDTNKFTLALTNRDEEPLDPARLSAGERQLLAISLLWGLAKVAGNRLPTVIDTPLGRLDSRH
REHLVDRYFPHAGRQVLLLSTDEEIDEHLLQRLRPSIAHSYVLVHDDTTFTTRVAEGYWWTEGALHAV
Length 628 aa
Homologues in dndDB  32 
Consensus based on Muscle-derived MSA in dndDB MAKMIIKQLTLENFGVFRGRHEIDLAPRERRNDKNGPVVGTERPIILFGGLNGAGKTTLLTAIRLALYGRLAFGSARGQQ
EYEEYLRELIHRGAGLGELPNGASIELEFTYNQGGHEHEYTVRRSWKAKGKKVKEKLSVEKDGQPLSELLYDQWQEFLNE
LIPPGIADLFFFDGEKIAELAEPDESGEVLKTAVRRLLGLDLIDRLRNDLGIFLRRQKSQQLDSSIKAQIEALEKEIKEL
ERQAEKLLQEAAFARSEIELLARDIEKLEKLLNAEGGAWAQTRAQEEQKVEALLAEKAELEKELRELIEGPLLPFALAPN
LLARLLKQLKAEQQIKQAASFEEELEKFLTELKSDLSAASRPSSTGEKAAEAIADDLKDRLAGKPKSGDLLLDISDREAN
QLQQLIEEVLQTAWQRFDELRKQLAELEEQLDQAAANIARAPEDEQIADLFEELRELDKKLEAAEAELRSLLEEAKQAKR
LAEDLERQLQKAHDKVRTFKDESNADRAVKNAQRTRNLLDEFSERLLQARVKQLEAEFLKSFKKLARKEDLILDAKIDPE
TFDVELIDEDGHEINRKRLSAGEKQILAIAILWALARTSGRRLPVIIDTPLGRLDSHHRDKLVENYFPTASHQVILLSTD
TEIDERYYVKLLKPDISHAYEIVFDAETKSSKIKEGYFWEETKEAAV
Length of Consensus 687 aa
NCBI-BLASTP similar proteins  52 
Putative conserved domains in pfam highlighted: PF02463, RecF/RecN/SMC N terminal domain


Pfam-A Matches:
Putative conserved domains in CCD cl09099: ABC_ATPase, ABC (ATP-binding cassette) transporter nucleotide-binding domain
Consensus match found in PDB by using PDBsum at EBI No significant hit found.
Literature
Literature
Other Literatures Yao F, Xu T, Zhou X, Deng Z, You D. (2009) Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1. FEBS Lett. 2009 Jan 24. [Abstract]

DNA phosphorothioation is widespread in many bacterial species. By homology analysis of the dnd gene cluster in Pseudomonas fluorescens Pf0-1, a spfBCDE gene cluster involved in DNA phosphorothioation was localized. Disruption of the spfD gene, a dndD homolog, caused the loss of the Dnd phenotype and demonstrated the involvement of spfD in DNA phosphorothioation in P. fluorescens Pf0-1. The ATPase activity of SpfD suggests that SpfD could hydrolyze ATP to provide the energy required in the DNA phosphorothioate modification process.
 
Interesting links TMHMM v. 2.0, Prediction of transmembrane helices in proteins
SignalP v3.0, Prediction of signal peptide cleavage sites
Jpred v3.0, protein secondary structure prediction
Last update 13/02/2009
PF00266 PF02662 PF04214