Conserved Protein Domain Family
KorB_N_like

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cd16398: KorB_N_like 
ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related domains
KorB, a member of the ParB like family, is present on the low copy number, broad host range plasmid RK2. KorB encodes a gene product involved in segregation of RK2 and acts as a transcriptional regulator, down-regulating at least 6 RK2 operons. KorB binds RNA polymerase and acts cooperatively with several co-repressors in modulating transcription. KorB is comprised of 3 domains, including a beta-strand C-terminal domain similar to SH3 domains and an alpha helical central domain that interacts with operator DNA. In ParB of P1 and SopB of F, the N-terminal region is responsible for interaction with the parA component. However, korB interaction with the RK2 parA-equivalent IncC has been mapped to the central HTH motif. This family is related to 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: 319256
View PSSM: cd16398
Aligned: 23 rows
Threshold Bit Score: 105.813
Threshold Setting Gi: 295698161
Created: 12-May-2015
Updated: 18-Aug-2016
Structure
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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
Evidence:
  • Comment:Motif identified in related ParB/Spo0J family proteins
  • Comment:partially conserved Spo0J motif
  • Comment:partial conservation of 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 45774      58 LDLIDEDPHQPRtadnpgFSPESIAEIGATIKE--------RGVKSPISVRENQeq------------------------ 105
gi 359751226  45 ISKIHPDPNNSRq----rVDPAKITELADSMKAvskvtgkqRGVKNPLSLKPHPel------------------------ 96
gi 408195392  47 LKKIHKDADNARk----tIDPQELRELADSMKSvnpatgkpRGNKNPVSLKPHPdi------------------------ 98
gi 110648047  37 WDKIEEDPDQPRt----hMDEDALKELADSMKQkgqn-gqpRGILQPISVRDNPnk------------------------ 87
gi 267986588  52 LDHFHEDEDNARq----eFDAQRLQELAESMTQvnpktgevRGILEPLSVKHHPdk------------------------ 103
gi 330427428  41 LDKIREDRNVRSenn-pgFGKVPMAELTADVKQ--------RGIKSPLSLRPDPer------------------------ 87
gi 442897162  51 IRNGDDSHAEDEe----aRQKFITEELGPDVKS--------RGVKSPISLRSDPen------------------------ 94
gi 695259724  30 ISDVMEDPKNARk----tYDPVKMAELTASVAQ--------SGVKSPISVKPHPsi------------------------ 73
gi 928773029   4 VARIHPDKNNKRrdgnqgLTKESIGEMAASIQErqr--qgkRGVMVPISLRPHPti------------------------ 57
gi 908371504  29 LDKIIPGKNPRTt-----FPPEKMERIAASIRE--------RRVKSPISVHAVSaeevathfeakglpfyyeskglaapt 95
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
Feature 1                  # ## ##                                  
gi 45774     106 --pGRYIINHGARRYRGSKWAGKk--SIPAFIDNdyNEADQVIENLQRNEL 152
gi 359751226  97 --eGEFMINAGYRRYLAAQEAGLd--TVPAFIDSdaDEYDNAVDNIQREGL 143
gi 408195392  99 --pGEYILNAGERRCAAAELAELp--DVLAFIDEdaDEFDNAVDNIQRVAL 145
gi 110648047  88 --pGYYLINHGHRRHRAQGLAGLkalPVPAILNNlsTQADQLLENIQREDL 136
gi 267986588 104 --pGHFIINGGARRYRAAKLAGLe--QAPYIIKDelDDFDKFVLNDQREQL 150
gi 330427428  88 --pGYYIINYGHRRYRSAKAAGAk--QVPGFIDTdfNSFDQVKENLKHEKL 134
gi 442897162  95 --pGKWLINHGENRWRATVWAELe--EIPAFIDEdyTDYDNAKENTKRLDV 141
gi 695259724  74 --pGKFLINFGHRRFRASKTAGLt--HVPAFIDEvhDDYDQVVENLQREDL 120
gi 928773029  58 --pGDFIINHGHRRYLGTIEAGLq--QIPGHEDHdfDDFDQVIENLQREKL 104
gi 908371504  96 eldGFYQINHGERRYRGSVMAGNk-eTIPAVLDDdhDGIDALVENIQRADL 145

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