1VZ0,1VZ0,1VZ0,4UMK


Conserved Protein Domain Family
SPO0J_N

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cd16393: SPO0J_N 
Click on image for an interactive view with Cn3D
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member
Spo0J (stage 0 sporulation protein J) is a ParB family member, a critical component of the ParABS-type bacterial chromosome segregation system. The Spo0J N-terminal region acts in protein-protein interaction and is adjacent to the DNA-binding domain that binds to parS sites. Two Spo0J bind per parS site, and Spo0J interacts with neighbors via the N-terminal domain to form oligomers via an Arginine-rich patch (RRXR). This superfamily 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: 319251
View PSSM: cd16393
Aligned: 65 rows
Threshold Bit Score: 123.748
Threshold Setting Gi: 12230415
Created: 21-May-2015
Updated: 18-Aug-2016
Structure
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Program:
Drawing:
Aligned Rows:
 
arginine patchputative ParB
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1: arginine patch [polypeptide binding site], 3 residue positions
Conserved feature residue pattern:R R RClick to see conserved feature residue pattern help
Evidence:
  • Comment:arginine patch mediates adjacent and transverse oligomerization
  • Comment:third residue typically hydrophobic
  • Comment:arginine patch shown to be critical for "spreading" in vivo and DNA-bridging in vitro in Bacillus subtilis

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                              ## #      
1VZ0_G        23 VVRLPLASIRPNPrQPRKRFAEESLKELADSIREKGLLQPLLVRPqg--------------dGYELVAGERRYRAALMAG 88
gi 311065159 172 LLDIPVSSIVPNAqQPRSVFDEEELNELAASIKEVGVLQPIVVRKrqagessksdvsretsqRYELIMGERRWRASQLAQ 251
gi 12230443   60 YREIALSDITENPcQPRQVFDDEAMSELVHSIREFGLLQPIVVRPasgs---------cgdtRYQIVMGERRWRAAQQAG 130
gi 302859178  29 MRDVGVEVIKADPrQPRKEFDEEALKELAESIKAHGLIQPIVLRPspd-----------kedEYYIIAGERRFRAVKLNG 97
gi 291165906   3 LQTIELQKIIPDPcQPRKFFDLAALEELASSIEQYGLLSPIIVRKqg--------------dRYIIVAGERRYRAMLLNK 68
gi 21222294   45 FAEVPLDAITPNPkQPRKDFDDDALAELVTSIREVGLLQPVVVRPte-------------pgRYELIMGERRFRACRELE 111
gi 319805121  26 VLEIALDKIERDEsQPRKNFDEDTLRDLAESIEAYGLLQPIVIRKkpn-----------aldRYIIVAGERRYRASQLLK 94
gi 456971445  51 VQNIPVSKIISKE-NPRKNFNSESLQELAESIKKYGLIQPISVRKig--------------nEYHLIAGERRLRATKLNG 115
gi 227236290  37 VASLPIEKVKPRPgQPRKDFDSKALEDLAHSIKEYGLLNPITVTKng--------------dYYEILAGERRYRATLLNQ 102
gi 404566790   8 YQDLDINLIKPDPeQPRKIFEDDSLTDLSNSIKATGVKQPITVRKvn--------------nEYMIIAGERRYRASILAN 73
                         90       100       110
                 ....*....|....*....|....*....|....*
Feature 1                                           
1VZ0_G        89 LQEVPAVVKDL----TDREa-lELALVENLQREDL 118
gi 311065159 252 LKTIPAIVKTTs---DDEMl--RDALLENLHRVAL 281
gi 12230443  131 LSFIPAIVRATg---DDSMl--RDALLENIHRVQL 160
gi 302859178  98 DKTIRAIVKKTl---KPEEi-gYVQMAENIKRANL 128
gi 291165906  69 MTHANCIVRNH----IDFR---EVSLIENVQREDL 96
gi 21222294  112 LDAIPAIVRATe---DEKLl--LDALLENLHRAQL 141
gi 319805121  95 ARTIKAVLLETn--pDDAEl-gYLQVIENIKRDAL 126
gi 456971445 116 EEFISSIVKNVh--qVDPDlipEYKLIENIHREDL 148
gi 227236290 103 ADTIDAIVKTYe--qKDIE---VLSLIENVQREDL 132
gi 404566790  74 KTTIPAVIIGDesqlTEEAl-yAHQLNENLHREDL 107

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