immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates immunoglobulin-binding eib genes in Escherichia coli. IbrB is related to the ParB N-terminal domain family, which includes DNA-binding proteins involved in chromosomal/plasmid segregation and transcriptional regulation, consistent with a possible mechanism for IbrB in DNA binding-related regulation of eib expression. The ParB like family is a diverse domain superfamily with structural and sequence similarity to ParB of bacterial chromosomes/plasmid parABS partitioning system and Sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes proteins related to StrR, a putative regulator in the biosynthetic gene cluster and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators SbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ) and EdeB (Brevibacillus brevis antimicrobial peptide edeine biosynthetic cluster). Nuclease activity has also been reported in arabidopsis Srx.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1149005034  46 PVDCVLWVKKEQLKPNNYNPNNVAPPEKRLLQVSIETDGFTQPIVVSPSSQNE-YEIVDGFHRHLVGKENGILgVRLKGY 124
Cdd:cd16397     1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDkYVIVDGFHRYTLAKKKPLI-ERLKGY 79

                          90       100
                  ....*....|....*....|.
gi 1149005034 125 LPVTCLDGNRHERIAATIRHN 145
Cdd:cd16397    80 LPVVVLDKDLEERMASTIRHN 100

immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates immunoglobulin-binding eib genes in Escherichia coli. IbrB is related to the ParB N-terminal domain family, which includes DNA-binding proteins involved in chromosomal/plasmid segregation and transcriptional regulation, consistent with a possible mechanism for IbrB in DNA binding-related regulation of eib expression. The ParB like family is a diverse domain superfamily with structural and sequence similarity to ParB of bacterial chromosomes/plasmid parABS partitioning system and Sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes proteins related to StrR, a putative regulator in the biosynthetic gene cluster and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators SbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ) and EdeB (Brevibacillus brevis antimicrobial peptide edeine biosynthetic cluster). Nuclease activity has also been reported in arabidopsis Srx.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1149005034  46 PVDCVLWVKKEQLKPNNYNPNNVAPPEKRLLQVSIETDGFTQPIVVSPSSQNE-YEIVDGFHRHLVGKENGILgVRLKGY 124
Cdd:cd16397     1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDkYVIVDGFHRYTLAKKKPLI-ERLKGY 79

                          90       100
                  ....*....|....*....|.
gi 1149005034 125 LPVTCLDGNRHERIAATIRHN 145
Cdd:cd16397    80 LPVVVLDKDLEERMASTIRHN 100

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1149005034   52 WVKKEQLKPNNYNPNNVAPPEKRLLQVSIETDGFTQPIVVSPsSQNEYEIVDGFHRHLVGKENGIlgvrlkGYLPVTCLD 131
Cdd:smart00470   2 EVPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIVRP-NDGRYEIIDGERRLRAAKLLGL------KEVPVIVRD 74

                           90
                   ....*....|....*
gi 1149005034  132 GNRHERIAATIRHNR 146
Cdd:smart00470  75 LDDEEAIALSLEENI 89

immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates immunoglobulin-binding eib genes in Escherichia coli. IbrB is related to the ParB N-terminal domain family, which includes DNA-binding proteins involved in chromosomal/plasmid segregation and transcriptional regulation, consistent with a possible mechanism for IbrB in DNA binding-related regulation of eib expression. The ParB like family is a diverse domain superfamily with structural and sequence similarity to ParB of bacterial chromosomes/plasmid parABS partitioning system and Sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes proteins related to StrR, a putative regulator in the biosynthetic gene cluster and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators SbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ) and EdeB (Brevibacillus brevis antimicrobial peptide edeine biosynthetic cluster). Nuclease activity has also been reported in arabidopsis Srx.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1149005034  46 PVDCVLWVKKEQLKPNNYNPNNVAPPEKRLLQVSIETDGFTQPIVVSPSSQNE-YEIVDGFHRHLVGKENGILgVRLKGY 124
Cdd:cd16397     1 PVDNVQWVPIEKVQANDYNPNKVAPPEMKLLKLSILEDGFTQPIVVYYDEEDDkYVIVDGFHRYTLAKKKPLI-ERLKGY 79

                          90       100
                  ....*....|....*....|.
gi 1149005034 125 LPVTCLDGNRHERIAATIRHN 145
Cdd:cd16397    80 LPVVVLDKDLEERMASTIRHN 100

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1149005034   52 WVKKEQLKPNNYNPNNVAPPEKRLLQVSIETDGFTQPIVVSPsSQNEYEIVDGFHRHLVGKENGIlgvrlkGYLPVTCLD 131
Cdd:smart00470   2 EVPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIVRP-NDGRYEIIDGERRLRAAKLLGL------KEVPVIVRD 74

                           90
                   ....*....|....*
gi 1149005034  132 GNRHERIAATIRHNR 146
Cdd:smart00470  75 LDDEEAIALSLEENI 89

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
                  ....*....|....*....|....*....|....*...
gi 1149005034  70 PPEKRLLQVSIETDGFTQPIVVSPSSQNEYEIVDGFHR 107
Cdd:cd16387     2 EEELEELAESIREHGVLQPIIVRPLPDGRYEIIAGERR 39

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. 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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1149005034  56 EQLKPNNYNPNNVAPPEKRLLQVSIETDGFTQPIVVSPSsqneYEIVDGFHRHLVGKENGILGVrlkgylPVTCLDG-NR 134
Cdd:cd16403     3 DDLKPYPRNARTHSEKQIEQLAASIREFGFTNPILVDED----GVIIAGHGRLLAAKLLGLKEV------PVIRLDHlSE 72

                          90
                  ....*....|..
gi 1149005034 135 HERIAATIRHNR 146
Cdd:cd16403    73 AQKRAYRIADNR 84

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 1149005034  63 YNPNNVAPPEKRLLQVSIETDGFTQPIVVSPssqnEYEIVDGFHRHLVGKENGI 116
Cdd:cd16404     7 FRTPNPTNEEFEELKESIRKNGIIVPIIVDQ----DGVIIDGHHRYRIAKELGI 56

ParB N-terminal, parA -binding, -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 1149005034  79 SIETDGFTQPIVVSPSSQNEYEIVDGFHRHLVGKENGILGV 119
Cdd:cd16408    23 SIKENGVLQPIIVRPIEDGKYEILAGHNRVNAAKLAGLTTI 63