InterPro : IPR012340

Name  Nucleic acid-binding, OB-fold Short Name  NA-bd_OB-fold
Type  Domain Description  A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease andaspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case [].There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 [].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



11 Child Features

Id Name Short Name Type
IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type NA-bd_OB_tRNA Domain
IPR022666 Ribosomal Proteins L2, RNA binding domain Rbsml_prot_L2_RNA-bd_dom Domain
IPR020189 Translation elongation factor, IF5A C-terminal Transl_elong_IF5A_C Domain
IPR011564 Telomeric single stranded DNA binding POT1/Cdc13 Telomer_end-bd_POT1/Cdc13 Domain
IPR012309 DNA ligase, ATP-dependent, C-terminal DNA_ligase_ATP-dep_C Domain
IPR002547 tRNA-binding domain tRNA-bd_dom Domain
IPR022967 RNA-binding domain, S1 S1_dom Domain
IPR029319 DNA ligase, OB-like domain DNA_ligase_OB Domain
IPR013849 DNA helicase, Holliday junction RuvA type, domain I, bacterial DNA_helicase_Holl-junc_RuvA_I Domain
IPR001059 Translation elongation factor P/YeiP, central Transl_elong_P/YeiP_cen Domain
IPR004150 NAD-dependent DNA ligase, OB-fold NAD_DNA_ligase_OB Domain

11 Contains

Id Name Short Name Type
IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type NA-bd_OB_tRNA Domain
IPR013955 Replication factor A, C-terminal Rep_factor-A_C Domain
IPR007199 Replication factor-A protein 1, N-terminal Rep_factor-A_N Domain
IPR011129 Cold shock protein Cold_shock_prot Domain
IPR019844 Cold-shock conserved site Cold-shock_CS Conserved_site
IPR018104 Translation initiation factor 1A (eIF-1A), conserved site TIF_eIF-1A_CS Conserved_site
IPR019979 Ribosomal protein S17, conserved site Ribosomal_S17_CS Conserved_site
IPR015365 Elongation factor P, C-terminal Elong-fact-P_C Domain
IPR018239 NAD-dependent DNA ligase, active site DNA_ligase_AS Active_site
IPR013852 Translation elongation factor P/YeiP, conserved site Transl_elong_P/YeiP_CS Conserved_site
IPR003871 Domain of unknown function DUF223 DUF223 Domain

42 Found In

Id Name Short Name Type
IPR004522 Asparagine-tRNA ligase Asn-tRNA-ligase Family
IPR002171 Ribosomal protein L2 Ribosomal_L2 Family
IPR005880 Ribosomal protein L2, bacterial/organellar-type Ribosomal_L2_bac/org-type Family
IPR001208 Mini-chromosome maintenance, DNA-dependent ATPase MCM_DNA-dep_ATPase Family
IPR013970 Replication factor A protein 3 Rfa2 Family
IPR004523 Aspartyl-tRNA synthetases Asp-tRNA_synthase Family
IPR006032 Ribosomal protein S12/S23 Ribosomal_S12/S23 Family
IPR001884 Translation elongation factor IF5A Transl_elong_IF5A Family
IPR008045 DNA replication licensing factor Mcm2 MCM2 Family
IPR013846 mRNA capping enzyme, C-terminal mRNA_cap_enzyme_C Domain
IPR001253 Translation initiation factor 1A (eIF-1A) TIF_eIF-1A Family
IPR000289 Ribosomal protein S28e Ribosomal_S28e Family
IPR008049 DNA replication licensing factor Mcm6 MCM6 Family
IPR004524 Aspartate-tRNA ligase, class IIb, bacterial/mitochondrial-type Asp-tRNA-ligase_IIb_bac/mt Family
IPR008050 DNA replication licensing factor Mcm7 MCM7 Family
IPR005570 RNA polymerase, Rpb8 RNA_pol_Rpb8 Family
IPR002313 Lysine-tRNA ligase, class II Lys-tRNA-ligase_II Family
IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb Asp/Asn-tRNA-synth_IIb Family
IPR005680 Ribosomal protein S23, eukaryotic/archaeal Ribosomal_S23_euk/arc Family
IPR000110 Ribosomal protein S1 Ribosomal_S1 Family
IPR004591 Replication factor A protein 1 Rfa1 Family
IPR005679 Ribosomal protein S12, bacteria Ribosomal_S12_bac Family
IPR008048 DNA replication licensing factor Mcm MCM5 Family
IPR008047 Mini-chromosome maintenance complex protein 4 MCM_4 Family
IPR008046 DNA replication licensing factor Mcm3 Mcm3 Family
IPR000424 Primosome PriB/single-strand DNA-binding Primosome_PriB/ssb Family
IPR012162 Polyribonucleotide nucleotidyltransferase PNPase Family
IPR011768 Translation elongation factor P Transl_elongation_fac_P Family
IPR014647 CST complex subunit Stn1 CST_STN1 Family
IPR011344 Single-stranded DNA-binding protein ssDNA-bd Family

0 Parent Features

3 Publications

First Author Title Year Journal Volume Pages
Ginalski K BOF: a novel family of bacterial OB-fold proteins. 2004 FEBS Lett 567 297-301
Draper DE RNA binding strategies of ribosomal proteins. 1999 Nucleic Acids Res 27 381-8
Agrawal V OB-fold: growing bigger with functional consistency. 2003 Curr Protein Pept Sci 4 195-206

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)