The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function

Kosinski, Jan; Feder, Marcin; Bujnicki, Janusz M

doi:10.1186/1471-2105-6-172

Table 1 New members of the PD-(D/E)XK superfamily Columns I and II contain accession numbers of Pfam and COG database entries corresponding to protein families analyzed in this work. Typically, COGs contain only subsets of seqeunces from the corresponding Pfam entries. Previously described molecular and/or cellular function and the newly predicted function is shown. * indicates only a general functional prediction based on the fact that a given protein family is found to possess a nuclease domain with a seemingly complete set of catalytic residues.

From: The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function

PFAM	COG	representative	closest homolog	other domains	known function	predicted function
02646	1322	E. coli RmuC	McrC	transmembrane helix, coiled-coil regions, unknown alpha/beta domain	limiting inversions at short-inverted repeats	cleaves DNA structures arising during recombination of short- inverted repeats
06054	4469	S. pneumoniae CoiA	COG 4636	unknown C-terminal domain	DNA uptake process and recombination	degradation of one DNA strand during DNA uptake
03749	1489	E. coli SfsA	YraN	OB-fold N-terminal domain	sugar fermentation stimulation	DNA cleavage*
-	2143 (KOG)	H. sapiens KIAA1018	AHJR	TPR-like domain, Rad18-like CCHC zinc finger, uknown 300aa domain	unknown	DNA repair, protein binding
06250	4804	E. coli YhcG	YraN	~200aa unknown N-terminal domain	unknown	DNA cleavage*
06356	-	Phage phi ETA orf25	TnsA or T7 EndoI	none	unknown	degradation of the host DNA upon lytic infection, production of recombinogenic fragments
-	5482	A. tumefaciens AGRL2570	AHJR	C-terminal domain with wHTH fold	unknown	DNA binding, DNA cleavage
06190	-	Phage PSA gp51	AHJR	none	unknown	recombinase
-	1395	P. abyssi PAB2104	AHJR	second inactive AHJRlike domain, HTH_3 domain	unknown	DNA cleavage or nicking*
-	4127	S. typhimurium STM4490	Mrr	putative inactivated nuclease domain	unknown	REase
	4741	T. volcanium TVN1166	YraN	N-terminal membrane helix	unknown	membrane-associated guardian against foreign DNA
06319	5321	A. tumefaciens AGR_C_8	AHJR	none	unknown	DNA cleavage*
05626	3372	P. abyssi PAB1046	AHJR	unknown ~250aa N-terminal domain	unknown	DNA repair or recombination
-	-	Phage T4 gp4	TnsA or T7 EndoI	none	important for the phage T4 head assembly process [52]	determination if DNA is packed properly into the phage head
-	-	P. aerophilum PAE1662	AHJR	none	unknown	type II REase

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ISSN: 1471-2105

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