1L1O,1QZH,1MJE,1IYJ,1MIU,1EYG,1GM5,1JMC,1JMC,1L1O,1L1O,1O7I,1OTC,1OTC,1OTC,1S40,1XJV,1XJV,2B3G,2I0Q,1OTC,2HPI,1IYJ,1IYJ,1MJE


Conserved Protein Domain Family
RPA2_OBF_family
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cd03524: RPA2_OBF_family 
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RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1).
Links
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Statistics
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PSSM-Id: 239601
Aligned: 65 rows
Threshold Bit Score: 30.0231
Created: 28-Mar-2006
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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generic bindinggeneric binding
Conserved site includes 19 residues -Click on image for an interactive view with Cn3D
Feature 1:generic binding surface I
Evidence:
  • Comment:Based on similarity to various OB folds with structures.
  • Comment:The generic binding surface I contains nucleic acid partners in most OB-fold complexes. In some cases, this surface may also contain the sites for protein-protein interaction.
  • Citation:PMID 8458342
  • Structure:1S40_A; Saccharomyces cerevisiae Cdc13 DBD binds telomeric ssDNA 11-mer; defined at 3.5A contacts.
  • Structure:1XJV_A; N-terminal OB-fold domain of human POT1 binds telomeric ssDNA; defined at 3.5A contacts.
  • Comment:The human POT1 protein consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA.
  • Structure:1MJE_A; Human BRCA2 fragment (containing an internal deletion) binds oligo(dT)9; defined at 3.5A contacts between the third OB fold (OB3) and ssDNA.
  • Comment:BRCA2 is a large nuclear protein consisting five structural domains, three of which are OB folds (OB1, OB2, and OB3). OB2 contains an internal insertion named the tower domain. For the BRCA2 fragment in the 1MJE_A structure, this insertion has been deleted.
  • Structure:1JMC_A; Human RPA1 binds octadeoxycytosine; defined at 3.5A contacts.
  • Comment:RPA1 has four OB-fold domains: DBD-A, -B, -C, and an N-terminal RPA1N domain. RPA1N (also called RPA70N) participates in specific protein-protein interactions, DBD-A and -B are the principal DNA binding domains, and DBD-C interacts with RPA2 and RPA3.
  • Citation:PMID 8990123
  • Structure:1GM5_A; Thermotoga maritime RecG binds a three-way DNA junction (a stalled replication fork mimic); defined at 3.5A contacts.
  • Structure:1OTC; Sterkiella nova heterodimeric TEBP binds telomeric ssDNA; defined at 3.5A contacts.
  • Comment:Oxytricha nova TEBP contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. Together with the two OB folds of the alpha subunit N-terminal domain, the beta subunit OB fold forms a deep cleft that binds ssDNA.
  • Citation:PMID 9875850
  • Structure:1EYG_D; Escherichia coli SSB monomer binds 35-mer ssDNA; defined at 3.5A contacts.
  • Comment:The E. coli SSB is a homotetramer that can bind long ssDNAs via a variety of binding modes, which differ in the number of nucleotides occluded per tetramer. The 1EYG structure shows E. coli SSB bound to two 35-mer ssDNAs.
Scroll to Sequence Alignment Display
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1          ###                                              #### #                    
1L1O_E     32 TIVGIIRHAekap--------------------------------------tniVYKIDDmt------------------ 55  human
1JMC_A     22 TICARVTNKsqirtwsn-----------------------------srgegklfSLELVDes------------------ 54  human
1L1O_F     28 SSVATVVYLrkencmyqacptqdcnkkvidqqnglyrcekcdtefpnfkyrmilSVNIADfq------------------ 89  human
1O7I_B     16 NVTVRVLEAsearqiqt-----------------------------kngvrtisEAIVGDet------------------ 48  Sulfolobus solfata...
1OTC_A    225 DVVAKILQVheld-------------------------------------eytnELKLKDas------------------ 249 Oxytricha nova
1S40_A     29 TMFGMLVSCsfdk-------------------------------------pafiSFVFSDftkndivqnylydr----yl 67  baker's yeast
1XJV_A    158 DLTCQLLGKaevd-------------------------------------gasfLLKVWDgtrtpfpswrvliqdlvleg 200 human
2B3G_A     25 KPILQVINIrpittg---------------------------------nsppryRLLMSDgl------------------ 53  human
NP_189742  19 RVQVRVLHTwktftm---------------------------------qfgetfDMVLSDvr------------------ 47  thale cress
Q06183    203 NVVGKVTQIvhrd-------------------------------------yytsDLRVKDts------------------ 227 Moneuplotes crassus

Feature 1                   ### #                                   #       ###              #
1L1O_E     56 ---------aaPM-DVRQWvdtddtss-------------------entvvppeTYVKVA-GHLRSfq--------nkKS 97  human
1JMC_A     55 ----------gEI-RATAFneqvdkf---------------------fplievnKVYYFSkGTLKIankqft-avkndYE 101 human
1L1O_F     90 ----------eNQ-WVTCFqesaeailgqnaaylgelkdkneqafeevfqnanfRSFIFR-VRVKVetyn----desrIK 153 human
1O7I_B     49 ----------gRV-KLTLWgkhag-------------------------sikegQVVKIEnAWTTAfk--------gqVQ 84  Sulfolobus solfata...
1OTC_A    250 ---------gqVF-YTLSLklkfp-------------------------hvrtgEVVRIRsATYDEtst-------qkKV 287 Oxytricha nova
1S40_A     68 idyenklelneGF-KAIMYknqfetfdsklrkifnn-glrdlqngrdenlsqygIVCKMN-IKVKMyn--------gkLN 136 baker's yeast
1XJV_A    201 dlshihrlqnlTI-DILVYdnhvhva----------------------rslkvgSFLRIYsLHTKLqsmnsenqtmlsLE 257 human
2B3G_A     54 ----------nTLsSFMLAtqlnplve--------------------eeqlssnCVCQIHrFIVNTlkd-------grRV 96  human
NP_189742  48 ---------gkKI-HASVKrehlnrf---------------------erpivrgEWRAIEnFGLTYatgqyk-atdhrYK 95  thale cress
Q06183    228 ---------kaTW-FLTVSrrkfp-------------------------rlyegVIIKIRsVNIDSeter-----ercLE 267 Moneuplotes crassus

Feature 1     ##             
1L1O_E     98 LVAf-------KIMP 105 human
1JMC_A    102 MTFnn----etSVMP 112 human
1L1O_F    154 ATVm-------DVKP 161 human
1O7I_B     85 LNAgs----ktKIAE 95  Sulfolobus solfataricus
1OTC_A    288 LILsh----ysNIIT 298 Oxytricha nova
1S40_A    137 AIVr-------ECEP 144 baker's yeast
1XJV_A    258 FHLhggtsygrGIRV 272 human
2B3G_A     97 VILm-------ELEV 104 human
NP_189742  96 MGFm------aQTHV 104 thale cress
Q06183    268 LAPh------sNIMT 276 Moneuplotes crassus

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