ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370739124  20 LLQVDWLKPHEEIVYSNYKELYDTISRSQVFLNPIIVDSSSWTVLDGMHRLAVAKSLGLRYVPAMTVDYFSD 91
Cdd:cd16400     1 LLPISDLRPHEEVDPDRVEELIEKILEEGVWTKPIIVDKNTGIILDGHHRLEAAKRLGLKRVPCVLLDYDDD 72

ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370739124  20 LLQVDWLKPHEEIVYSNYKELYDTISRSQVFLNPIIVDSSSWTVLDGMHRLAVAKSLGLRYVPAMTVDYFSD 91
Cdd:cd16400     1 LLPISDLRPHEEVDPDRVEELIEKILEEGVWTKPIIVDKNTGIILDGHHRLEAAKRLGLKRVPCVLLDYDDD 72

ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid protein ParB and mammalian Sulfiredoxin-1. ParB is involved in chromosome partition. It localizes to both poles of the predivisional cell following completion of DNA replication. Sulfiredoxin-1 contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370739124  38 KELYDTIsRSQVFLNPIIVD---SSSWTVLDGMHRLAVAKSLGLRYVPAMtVDYFSDSIRV 95
Cdd:pfam02195  24 EELAASI-KKRGLLQPIIVRktpDGRYEIIAGERRLRAAKLLGLKEVPVI-VREIDDEEAI 82

ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370739124  20 LLQVDWLKPHEEIVYSNYKELYDTISRSQVFLNPIIVDSSSWTVLDGMHRLAVAKSLGLRYVPAMTVDYFSD 91
Cdd:cd16400     1 LLPISDLRPHEEVDPDRVEELIEKILEEGVWTKPIIVDKNTGIILDGHHRLEAAKRLGLKRVPCVLLDYDDD 72

ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5-->3 exonuclease activity.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370739124   26 LKPHEEIVYSN----YKELYDTIsRSQVFLNPIIVDSSS--WTVLDGMHRLAVAKSLGLRYVPAMTVDYFSD 91
Cdd:smart00470   8 LRPNPDQPRLTseesLEELAESI-KENGLLQPIIVRPNDgrYEIIDGERRLRAAKLLGLKEVPVIVRDLDDE 78

pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ParB acts in a plasmid partitioning system made up of 3 parts: AspA, ParA motor protein, and ParB, which links ParA to the protein-DNA superhelix. As demonstrated in Sulfolobus, AspA spreads along DNA, which allows ParB binding, and links to the Walker-motif containing ParA motor protein. The Sulfolobus ParB C-terminal domain resembles eukaryotic segregation protein CenpA, and other histones. This family is related to the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system and related proteins.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1370739124  37 YKELYDTIsRSQVFLNPIIVDSSsWTVLDGMHRLAVAKSLGLRYVPAMTVD 87
Cdd:cd16404    17 FEELKESI-RKNGIIVPIIVDQD-GVIIDGHHRYRIAKELGIKEVPVIVYD 65

ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain/Sulfiredoxin (Srx) superfamily contains proteins with diverse activities. Many of the families are involved in segregation and competition between plasmids and chromosomes. Several families share similar activities with the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system. Also within this superfamily is sulfiredoxin (Srx; reactivator of oxidatively inactivated 2-cys peroxiredoxins), RepB N-terminal domain (plasmid segregation replication protein B like protein), nucleoid occlusion protein, KorB N-terminal domain partition protein of low copy number plasmid RK2, irbB (immunoglobulin-binding regulator that activates eib genes), N-terminal domain of sopB protein (promotes proper partitioning of F1 plasmid), fertility inhibition factors OSA and FiwA,DNA sulfur modification protein DndB, and a ParB-like toxin domain. Other activities includes a StrR (regulator in the streptomycin biosynthetic gene cluster), and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators sbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ). Nuclease activity has also been reported in Arabidopsis Srx.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1370739124  36 NYKELYDTIsRSQVFLNPIIV---DSSSWTVLDGMHRLAVAKSLGLRYVPAM 84
Cdd:cd16387     4 ELEELAESI-REHGVLQPIIVrplPDGRYEIIAGERRWRAAKLAGLTTIPVV 54

ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370739124  51 LNPIIVDSSS---WTVLDGMHRLAVAKSLGLRYVPAMTVDYFSD 91
Cdd:cd16409    19 LTPITVRQDPggrYTLIAGAHRLAAAKLLGWDTIDAIIVKADDL 62