Conserved Protein Domain Family
ParB_N_like

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cd16410: 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.
Statistics
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PSSM-Id: 319267
View PSSM: cd16410
Aligned: 20 rows
Threshold Bit Score: 99.5826
Threshold Setting Gi: 373873305
Created: 12-Feb-2016
Updated: 18-Aug-2016
Structure
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Aligned Rows:
 
putative ParBarginine
Feature 1: putative ParB Box II like Motif [polypeptide binding site], 5 residue positions
Conserved feature residue pattern:G R R [REQ] AClick to see conserved feature residue pattern help
Evidence:
  • Comment:Motif identified in related ParB/Spo0J family proteins
  • Comment:third R often replaced with Q, E in this family
  • Comment:motif partially matches Bacillus subtilis ParB Box II, shown to be essential for DNA loop formation in vitro and Spo0J complex formation in vivo
  • 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
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                   # ## ##                              
gi 500540212   5 IHKIKVSDRIRKEFGNIEELAMDIKEnGLINPPVVTpDHELIAGERRLRACKHLNYQQIEVRVMSVRDye-hKLKIEIGE 83
gi 573531553   5 INKIKVSDRIRKDFGGIEELAQDIDQnGLINPILVTpDYQLIAGERRLRAHQVLGRKEVVVRVMEISDfe-hQLRLEISE 83
gi 560394776   5 INKIIIKDRIRKDYGNIEELAKDIKEnGLINPPVVTpEYILIAGERRTKACKYLGYEQIEVRVMTVKDal-hQLKLEISE 83
gi 383107634   5 VQDIRIGKRIRHDIGDISSLKESMKRyGMLNPVVITeSGTLIAGYRRLQAARELGWSTVRVKIMPNTDea-dLIEIEIDE 83
gi 565680775   5 IQEIQIKNRIRKNLGDLAGLKDSIQKhGILNPVVINsKNELVAGHRRLESARQLGWNMIPVRIIDEKDaa-dKVEIEIEE 83
gi 689726427   5 VSEIIIRDRIRKNLGDLSGLMESISKhGLMNPIVVNsKKELIAGHRRLESVRRLGWETIQVRVITNLDsa-tNLEMEIEE 83
gi 573547387   5 IHTINIGSRIREDMGDIAGLAESINArGLLHPIVIDeSGNLIAGHRRLEAHKLLGREEVETRTIADLTek-eKRLIELEE 83
gi 296180752   8 LDAITVEGRHRKDLGDLQALADSIKTvGLLHPVVVTpDGQLVAGQRRVEAVKLLGWQRVPVTVMADLDdaarLLRAESDE 87
gi 306532138   5 IGRIRIPKRIRKDVGDLSPLKESMKKhGLLHPIIISrDFDLIAGYRRLRAAQELGWKTIEVRIVPIDDem-gMRELEMEE 83
gi 373873305  30 IRDIRIPRRIRKRKIQIDDLVESIAEfGLLQPIIVDtENTLIAGYRRLEAARALGWESIDVRVIDAPErk-dRLLLEIEE 108

                 .
Feature 1         
gi 500540212  84 N 84
gi 573531553  84 N 84
gi 560394776  84 N 84
gi 383107634  84 N 84
gi 565680775  84 N 84
gi 689726427  84 N 84
gi 573547387  84 N 84
gi 296180752  88 N 88
gi 306532138  84 N 84
gi 373873305 109 N 109

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