Summary: Replication factor-A protein 1, N-terminal domain
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Replication factor-A protein 1, N-terminal domain Provide feedback
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This tab holds annotation information from the InterPro database.
InterPro entry IPR007199
Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [PUBMED:7753855].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||nucleus (GO:0005634)|
|Molecular function||DNA binding (GO:0003677)|
|Biological process||DNA replication (GO:0006260)|
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The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin . The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands .
The clan contains the following 58 members:BOF BRCA-2_OB1 BRCA-2_OB3 CSD DNA_ligase_A_C DNA_ligase_OB DNA_ligase_OB_2 DUF2110 DUF223 DUF3127 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 mRNA_cap_C NlpE_C OB_aCoA_assoc OB_NTP_bind OB_RNB PCB_OB Phage_DNA_bind POT1 RecG_wedge RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rep_fac-A_C REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 Ribosomal_S28e RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RsgA_N RuvA_N S1 S1-like S1_2 SSB SSL_OB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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- alignment generated by searching the metagenomics sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Pfam-B_6000 (release 7.3);|
|Author:||Wood V, Finn RD|
|Number in seed:||11|
|Number in full:||554|
|Average length of the domain:||97.30 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||16.46 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Rep-A_N domain has been found. There are 22 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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