1JMC,1FGU


Conserved Protein Domain Family
RPA1_DBD_B
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cd04475: RPA1_DBD_B 
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RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can.
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Statistics
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PSSM-Id: 239921
Aligned: 48 rows
Threshold Bit Score: 67.9946
Created: 5-Jun-2006
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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ssDNA bindingDBD-B/DBD-A
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:ssDNA binding site [nucleic acid binding site]
Evidence:
  • Comment:RPA1 has four OB-fold domains: RPA1 DBD-F, -A,-B, and C. RPA1 DBD-A and -B are the principal DNA binding domains.
  • Structure:1JMC_A; Human RPA1 DBD-B binds octadeoxycytosine; defined at 3.5A contacts.
  • Citation:PMID 8990123
  • Comment:The tandem orientation of the two OB-folds (DBD-A and -B) is stabilized by the presence of DNA.
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                                                    # #                                  
1JMC_A        140 LVDIIGICKSYEDATKITvrsnnrEVAKRNIYLMDTSgkVVTATLWG----------EDADKFDGSr----------QPV 199  human
BAE00606      167 IINVLAAVKSVGEPKYFTtsd-rrKGQRCEVRLYDETefSFAMTCWD----------NESILLAQSwm-------prETV 228  crab-eating m...
AAG00003      241 PIDVLVCIKEFKDVENYTpte-nkPPHKRHIQVIDDSksEIRATFWG----------YNAVDAIREef--------lNKV 301  nematode
XP_952613     317 TIDVIAIVVTARDLQKINnkatgnNVEKRDFLLCDSTntTVWVTSWG----------QKTQLFNYEgd-------nsHPL 379  Theileria ann...
AAB63407      353 LIDVLVVVEKMDPEATEFtskagkSLIKREMELIDESgaLVRLTLWG----------DEATKALVDdy--------vQKV 414  nematode
NP_702753     816 FVDIIAVVLNYQEKMQIFvkktgqYKDKRDVTLIDESfdTIQVTLWE----------KNATIIDEMnl-------rdNCI 878  Plasmodium fa...
EAT37860      171 NVNVLVVVRAIRPSKQIViaktgkLKNLREVIVMDAShgGMSMKFWNse------yvQRIDKWIPM-----------TTV 233  yellow fever ...
CAD70895      216 LTNILVCVSSIGPRKTIKannkpsTLELVEVHVCDETd-HCVLKLWS----------DQIVSAREWta--------gQTI 276  Neurospora cr...
XP_001027159  215 HFDILGVVMEEPSKERVKdse-grELDTIKFLIGDETrhTLQVSIRN----------EYGLNLNLKi----------FDV 273  Tetrahymena t...
XP_001213108  186 TVNLIVGVVTIRPPRRIVtkqwkkELDLVEVVVGDETrsGFGVTFWLppeartvtgkDDIETKAGHelrhtletlrpRDI 265  Aspergillus t...

Feature 1                   #   #       #           #                     
1JMC_A        200 LAIKg----ARVSDFg--gRSLSVLs--------SSTIIANpd-iPEAYKLRGWFD 240  human
BAE00606      229 IFVSd----VRISFD----KFRNCMtat----viSKTIITTnpetPEANILLNFIR 272  crab-eating macaque
AAG00003      302 VAFKg----VIPTEGnvprNSRKMLcdafqrefyQTPIDILvf-vQDMDETCSDYN 352  nematode
XP_952613     380 VCLKg----VKVGEWq--gKKLDVQi--------STQVICEpv-iPEALKLRKWWN 420  Theileria annulata strain Ankara
AAB63407      415 IAFKg----VIPREFng-gFSLGTG---------SATRIISvpeiAGVSELYDWYA 456  nematode
NP_702753     879 VCFKy----LKIGEWq--gKKLESHa--------RTKIEINpdniEKAYILKNWWI 920  Plasmodium falciparum 3D7
EAT37860      234 LLIMd----VRIEYNqy-hKSVCLGm-------sGKTIITEdpavEEADQLLLHVM 277  yellow fever mosquito
CAD70895      277 LLITnpklyPRKKGN----ENPGLGva------lNSIVDVDpd-fPDAHWLRRMAE 321  Neurospora crassa
XP_001027159  274 VLIKst--hVNVYANq---KSVDSG---------SGILVNPd--iQQALDLLYSFE 313  Tetrahymena thermophila SB210
XP_001213108  266 VLLRm----VGLSTFre-rVYGQSLrk------gITTVELLhrqrVDATDVGGRYS 310  Aspergillus terreus NIH2624

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