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

DndA DndB DndC DndD DndE
Dnd protein DndA
Putative function Cystein desulfurtransferse, provides S via an L-cysteine desulfurylase activity (64% identity to IscS/NifS)
DndA sequence of Streptomyces lividans 1326 MTYGTCRLTLKGGLGSMVTYLDAAATTRVDQRVADIVLHWMTAEFGNAGSRHEYGIRAKRGVERAREYLASTVSAEPDEL
IFTSGATESNNIALLGLAPYGERTGRRHIITSAIEHKAVLEPLEHLAGRGFEVDFLTPGPSGRISVEGVMERLRPDTLLV
SLMHVNNETGVIQPVAELAQQLRATPTYLHVDAAQGYGKVPGDLTTPIDMISISGHKIGAPKGVGALVTRRREEMDDERV
PLEPIMFGGGQERKLRPGTLPVPLIMGLAEAAKIFEAEHAQWQVAAQDLRSRLLAGLASTSFQVNGDQDHVVPHILNLSF
EDVDAEAFLVTLKDLVAVATGSACTSASFTPSHVLRAMGLPEEAASKSLRFSWTPGQATDLDVEELARGVAKLKPSY
Length 397 aa
Homologues in dndDB  12 
Consensus based on Muscle-derived MSA in dndDB MSSPIYLDCNATTPVDPEVAEVMLPYLTEDFGNAGSRTHEFGARAKKAVEKARAQVAELVGAKPDEVIFTSGATESNNIA
ILGLAEAGEEKGKKHIITSAIEHKAVLEPCEHLEKNGFEVTFLPVDESGRVSLEEIADALRDDTLLVSIMHVNNETGVIQ
PIAEIAEILEEHGAFFHTDAAQGFGKIPDDLKNKPIDLISISGHKIYGPKGIGALVIRRRGKPKVPLAPIMFGGGQERGL
RPGTLPVPLIAGLGEAAEIAEKNLAKWQKAARALRDQLLDALKTLLPAQLNGDQAHRLPHILNFSFPGVDAEALIVMLKD
DVAISAGSACTSSSYEPSHVLKAMGLDEDRARGALRFSWGHGTSEDDIIIDILEIAEKLAKLKP
Length of Consensus 384 aa
NCBI-BLASTP similar proteins  243 
Putative conserved domains in pfam highlighted: PF00266, Aminotransferase class-V


Pfam-A Matches:
PF00266 PF02662 PF04214
Putative conserved domains in CCD cl00321: Aminotran_1_2 Super-family
Consensus match found in PDB by using PDBsum at EBI PDB code: 1p3w, Cysteine desulfurase. Chain: b, a. Synonym: thii transpersulfidase, nifs protein homolog.
Literature D. You, L. Wang, F. Yao, X. Zhou, and Z. Deng (2007). A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron-sulfur cluster protein in Streptomyces lividans. Biochemistry, 46(20):6126-33. [Abstract] [Full Text]

A novel DNA modification system by sulfur (S) in Streptomyces lividans 66 was reported to be encoded by a cluster of five genes designated dndA-E [Zhou, X., He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann, J. D., and Deng, Z. (2005) Mol. Microbiol. 57, 1428-1438]. The dndA gene was cloned and the protein product expressed in Escherichia coli, purified to homogeneity, and characterized as a homodimeric protein of ca. 91 kDa. Purified DndA has a yellow color and UV-visible spectra characteristic of a pyridoxal phosphate-containing enzyme and was proven to be a cysteine desulfurase able to catalyze removal of elemental S atoms from L-cysteine to produce L-alanine with substrate specificity similar to that of E. coli IscS. DndC was also purified to homogeneity and found to contain a 4Fe-4S cluster by spectral analysis and have obvious ATP pyrophosphatase activity. DndA could catalyze iron-sulfur cluster assembly by activation of apo-Fe DndC protein prepared by removal of its iron-sulfur cluster using ,'-dipyridyl. A mutated DndA, with serine substituted for cysteine at position 327, which was confirmed to have lost its corresponding cysteine desulfurase activity, also lost its ability to reactivate the apo-Fe DndC. The likely involvement of an interaction between DndA and DndC in the biochemical pathway for the unusual site-specific DNA modification in S. lividans 66 is discussed.
 
Other Literature D.L. You, T.G. Xu, F. Yao, X.F. Zhou, and Z.X. Deng (2008) Direct evidence that ThiI is an ATP pyrophosphatase for the adenylation of uridine in 4-thiouridine biosynthesis. Chembiochem, 9(12):1879-82. [Abstract]
ThiI is an enzyme that plays a role in the biosynthesis of both thiamin and 4-thiouridine at position 8 in bacterial tRNA. Using kinetic assays and mass spectrometry, we have identified ThiI as ATP pyrophosphatase that catalyzes the hydrolysis of ATP to AMP and pyrophosphate. Our results provide a direct evidence for the formation of adenylation intermediate in the tRNA modification process.
 
Cross-references Sequence database UniProtKB search: dndA
Protein family database InterPro: IPR017644 Cysteine desulfurase, DndA
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 1p3w 1eg5 1ecx 2hdy