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

DndA DndB DndC DndD DndE
Dnd protein DndB
Putative function Putative Fe-S cluster binding protein, affects modification specificity as transcriptional regulator
DndB sequence of Streptomyces lividans 1326 MNKGRLPALTRYLVDNPTDYVFSALTASVDGDMRFEGIADSGVGMRAGQIVISMAARFLINDGQHRRAAIEQALKENPDL
GEETIAVVFFHDAGLARCQQMFADLNRHAVRPPRSIGVLYDHRDDLATTVRLLAMRAPVFKGFVEMESSTLSQRSRKLFT
LSSVYYATQSLLQGLEITKDQSRELAEAYWAAVDAVIPEWKLVRRRELSAQDVRRDYLHTHGIALHALGRVGNSLLRKSL
APRSWTPALKRLSSVDWSRANTDWEGRALVGGRVSKSHQNLTLTVNYLRQHLKLELSAEEQRAEDAYLRGES
Length 312 aa
Homologues in dndDB  32 
Consensus based on Muscle-derived MSA in dndDB KALMMASMDSGYCYSFPAIRGIQAGREFYIAMCPLRIIPKIFSFDEDEVPPELRAQRTLNKSRIPEIARYLLENPKDYVF
SALTASIDGDVEFEPFPGSGPAHFNLGTLRIPMDAQILINDGQHRRAAIEEALKERPELGHETIPVVFFVDEGLKRSQQM
FADLNKYAVRPSPSLGVLYDHRDALAELARYLAMSVEPFKGLTEMEKSSLSPRSRKLFTLSSIKQATRALLGKDAKDDFT
EEEKQLATEFWEAVAENMPDWQLVRKKEVSPGELRQDYIHAHGIGLQALGRAGNSLLREYPEAWKEKLKALKTIDWSRSN
APDWEGRAMNGGKVSKSSTNITLTCNYLKKALGLPLTPEEQALEDQFLASRAALGVA
Length of Consensus 377 aa
NCBI-BLASTP similar proteins  19 
Putative conserved domains in pfam

No conserved domains identified.
Putative conserved domains in CCD No conserved domains identified.
Consensus match found in PDB by using PDBsum at EBI No significant hit found.
Literature J. Liang, Z. Wang, X. He, J. Li, X. Zhou, and Z. Deng (2007). DNA modification by sulphur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Research, 35(9):2944-54. [Abstract] [Full Text]

The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change from a preferential modification site in strain 1326 to more random modifications in the mutant. Fourteen randomly modifiable sites on pHZ209 were localized, and each seemed to be able to be modified only once. Residues in a region (5'-c-cGGCCgccg-30) including a highly conserved 4- bp central core (5'-GGCC-3') in a well-documented preferential modification site were assessed for their necessity by site-directed mutagenesis. While the central core (GGCC) was found to be stringently required in 1326 and in the mutant, 'gccg' flanking its right could either abolish or reduce the modification frequency only in the mutant, and two separate nucleotides to the left had no dramatic effect. The lack of essentiality of DndB for S- modification suggests that it might only be required for enhancing or stabilizing the activity of a protein complex at the required preferential modification site, or resolving secondary structures flanking the modifiable site(s), known to constitute an obstacle for efficient modification.
Cross-references Sequence database UniProtKB search: dndB
Protein family database InterPro: IPR017642, DndB
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 30/09/2008
PF00266 PF02662 PF04214