Conserved Protein Domain Family

cd16406: ParB_N_like 
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.
PSSM-Id: 319263
View PSSM: cd16406
Aligned: 97 rows
Threshold Bit Score: 64.8461
Threshold Setting Gi: 77462630
Created: 27-Mar-2015
Updated: 18-Aug-2016
Aligned Rows:
putative ParBarginine patch
Feature 1: putative ParB Box II [polypeptide binding site], 5 residue positions
Conserved feature residue pattern:G R R [RKH] AClick to see conserved feature residue pattern help
  • Comment:partially conserved motif similar to Bacillus subtilis ParB Box II, shown to be essential for DNA loop formation in vitro and Spo0J complex formation in vivo
  • Comment:Motif identified in related ParB/Spo0J family proteins
  • Comment:Mutations in B. subtilis (R79A, R80A, R82A) incapacitate Spo0J spreading from parS sites
  • Comment:ParB box may interact with a negatively charged region of another Spo0J molecule
  • Citation:PMID 9915704

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
Feature 1                                                   # ## ##                              
gi 474937014  46 YSTIGVSELADSIEAvGLLQNLTVRkg-------kkGKYEVVAGSRRLAALRLLVKEgrla-------------ddaEIP 105
gi 74419322   22 FDPATIEGLAASIRQdGLLQNLVVRps-------rgRQFRIVSGERRYRALKLLQERgdia-------------edfGVT 81
gi 563228394  22 FDERSIAGLAQSIKCdGVIQNLTVVpe-------gdGRYRVHIGKRRFLALQLLKRRgdid-------------elyQVP 81
gi 587637703 114 FDPAAVAEIADSIAAkGLLQPLTIRagtrdildavgQLAEVYIGGTRYRALKLLHDEgrwped---------rlpggMVP 184
gi 429132753  46 FDDKTLFELATDIHHkGILQNLVVRphp-----tedGAFEIAAGERRYRAVGLLVDGlelvdenggestvlkvgadyLMP 120
gi 288911705 103 CDPEGIASLAASIEAqGLMQNLVLRrsd-----eagVAYQIVAGERRFRALRLLAEQgkwn------------peepNIP 165
gi 761898586  25 LTPSAIEAMATSLAAkGQIMPIVVHpmk-----grkDKFGVFAGQRRYRAFKALIEAgrlp-------------rdhPID 86
gi 722248456   8 PDAEETSALQASILAdGLLNPIAVHpmk-----gskTKWGAVAGGRRYRAIKALVKNgdlp-------------adyGVK 69
gi 523375363  23 HDANAITGMAESLATrGQLYPLVVHpmpak--rgkkRSYGALAGGRRLRAFALLIEQgrlp-------------sdhPID 87
gi 388531400  55 IDDEAIAELARTMEEhGQLQPILVRrdp------adRRHYVIVAGERRYRAARLNGW--------------------PTL 108
                         90       100
Feature 1                                
gi 474937014 106 CNVRNt---dNHTELSLAENVQRE 126
gi 74419322   82 VEIRSklskdDALRLATVENVQRE 105
gi 563228394  82 VDIREnlegrDALRIAAVENVQRE 105
gi 587637703 185 CTLREcs-diELIEIALTENIQRQ 207
gi 429132753 121 VKVQPlt-dlQLLEIATTENLQRD 143
gi 288911705 166 GNLIDad-daKHLAIALLENLQRH 188
gi 761898586  87 AMVREaetegDLIALSTAENAIRW 110
gi 722248456  70 VTILEglsdaELIEQSITENLIRR 93
gi 523375363  88 VIVRDitdkgELHELSLFENLVRV 111
gi 388531400 109 LAIEHd---aDPEIAALIENLQRV 129

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