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InterPro: IPR012340 Nucleic acid-binding, OB-fold

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UniProtKB
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50724 proteins
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IPR012340 NA-bd_OB-fold
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Domain
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InterPro RelationshipsHelp
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Parent IPR016027 Nucleic acid-binding, OB-fold-like
Children IPR000266 Ribosomal protein S17
IPR001059 Translation elongation factor P/YeiP, central
IPR002547 tRNA-binding domain
IPR003029 Ribosomal protein S1, RNA binding domain
IPR004150 NAD-dependent DNA ligase, OB-fold
IPR006196 S1, IF1 type
IPR011564 Telomere end binding protein
IPR012309 ATP dependent DNA ligase, C-terminal
IPR013849 DNA helicase, Holliday junction RuvA type, domain I, bacterial
IPR020189 Translation elongation factor, IF5A C-terminal
Found in IPR000110 Ribosomal protein S1
IPR000289 Ribosomal protein S28e
IPR000424 Primosome PriB/single-strand DNA-binding
IPR001208 DNA-dependent ATPase MCM
IPR001253 Translation initiation factor 1A (eIF-1A)
IPR001884 Translation elongation factor, IF5A
IPR002171 Ribosomal protein L2
IPR002313 Lysyl-tRNA synthetase, class II
IPR003512 Phage DNA binding/helix destabilising
IPR004329 CcmE/CycJ protein
IPR004522 Asparaginyl-tRNA synthetase, class IIb
IPR004523 Aspartyl-tRNA synthetase, class IIb, archea/euk type
IPR004524 Aspartyl-tRNA synthetase, class IIb, bacterial/mitochondrial type
IPR004591 Replication factor-a protein 1 Rpa1
IPR005570 RNA polymerase, Rpb8
IPR005679 Ribosomal protein S12, bacterial-type
IPR005680 Ribosomal protein S23, eukaryotic/archaeal
IPR005880 Ribosomal protein L2, bacterial-type
IPR006032 Ribosomal protein S12/S23
IPR008045 MCM protein 2
IPR008046 MCM protein 3
IPR008047 MCM protein 4
IPR008048 MCM protein 5
IPR008049 MCM protein 6
IPR008050 MCM protein 7
IPR011344 Single-strand DNA-binding
IPR011768 Translation elongation factor P
IPR011897 Translation elongation factor P-like, YeiP
IPR012156 Cold shock, CspA
IPR012162 Polyribonucleotide nucleotidyltransferase
IPR012751 CspD, cold shock
IPR013846 mRNA capping enzyme, C-terminal
IPR013970 Replication factor A protein 3
IPR014646 Replication protein A, subunit RPA32
IPR014647 Uncharacterised protein, OB-fold-containing
IPR015363 CDC13, ssDNA binding
IPR016306 DNA ligase, bacteriophage
IPR016411 Helix-destabilising protein
IPR017075 mRNA capping enzyme, alpha subunit
IPR018032 Ribosomal S1 synthesis/modification protein
IPR020564 Aspartyl-tRNA synthetase, class IIb, bacterial-type
IPR020599 Translation elongation factor P/YeiP
IPR020780 Aspartyl-tRNA synthetase, class IIb, archaeal type
IPR020923 DNA ligase B
Contains IPR004365 Nucleic acid binding, OB-fold, tRNA/helicase-type
IPR007199 Replication factor-A protein 1, N-terminal
IPR011129 Cold shock protein
IPR013852 Translation elongation factor P/YeiP, conserved site
IPR013955 Replication factor-A, C-terminal
IPR015365 Elongation factor P, C-terminal
IPR018104 Translation initiation factor 1A (eIF-1A), conserved site
IPR018239 NAD-dependent DNA ligase, active site
IPR019844 Cold-shock conserved site
IPR019979 Ribosomal protein S17, conserved site
InterPro annotation
BioMart Logo Entry Details in BioMart
AbstractHelp
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A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-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 [1]. 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 [2].

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 [3].
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PDB - click here
1a0i , 1a1d , 1ae2 , 1ae3 , 1asy , 1asz , 1b04 , 1b70 , 1b7y , 1b8a , 1bbu , 1bbw , 1bdx , 1bkb , 1bvs , 1c04 , 1c0a , 1c7y , 1c9o , 1ckm , 1ckn , 1cko , 1csp , 1csq , 1cuk , 1d7q , 1d8l , 1dgs , 1e1o , 1e1t , 1e22 , 1e24 , 1e3p , 1e7z , 1efw , 1eiy , 1eov , 1eqq , 1eqr , 1euj , 1ewi , 1eyg , 1ffk , 1fgu , 1fjg , 1fl0 , 1fvi , 1g29 , 1g51 , 1g6p , 1gd7 , 1gix , 1giy , 1gkh , 1go3 , 1gvp , 1h95 , 1hh2 , 1hjp , 1hnw , 1hnx , 1hnz , 1hr0 , 1hz9 , 1hza , 1hzb , 1hzc , 1i3q , 1i50 , 1i5f , 1i6h , 1i94 , 1i95 , 1i96 , 1i97 , 1ibk , 1ibl , 1ibm , 1il2 , 1ixr , 1iz6 , 1j5e , 1j6q , 1jb7 , 1je5 , 1jgo , 1jgp , 1jgq , 1jj2 , 1jjc , 1jjg , 1jmc , 1jt8 , 1k0r , 1k73 , 1k83 , 1k8a , 1k8g , 1k9m , 1kaw , 1kc8 , 1kd1 , 1khi , 1kix , 1kl9 , 1kqs , 1krs , 1krt , 1kxl , 1l0w , 1l1o , 1l2f , 1lm0 , 1luz , 1lyl , 1m1k , 1m90 , 1mjc , 1mkh , 1n32 , 1n33 , 1n34 , 1n36 , 1n8r , 1n9w , 1ne3 , 1nik , 1nji , 1nkw , 1nmf , 1nmg , 1nt9 , 1ntg , 1nwx , 1nwy , 1ny4 , 1o7i , 1otc , 1oxs , 1oxt , 1oxu , 1oxv , 1oxx , 1p16 , 1p8l , 1pa6 , 1pfs , 1ph1 , 1ph2 , 1ph3 , 1ph4 , 1ph5 , 1ph6 , 1ph7 , 1ph8 , 1ph9 , 1phj , 1pns , 1pnx , 1pqv , 1pyb , 1pys , 1q46 , 1q7y , 1q81 , 1q82 , 1q86 , 1q8k , 1quq , 1qvc , 1qvf , 1qvg , 1qzg , 1qzh , 1r5u , 1r9s , 1r9t , 1rip , 1rl2 , 1s3o , 1s40 , 1s72 , 1se8 , 1sfo , 1slj , 1sm1 , 1smx , 1sn8 , 1sr3 , 1sro , 1sru , 1ta8 , 1tae , 1twa , 1twc , 1twf , 1twg , 1twh , 1txy , 1ue1 , 1ue5 , 1ue6 , 1ue7 , 1ueb , 1v1q , 1v43 , 1v9p , 1vci , 1vow , 1vq4 , 1vq5 , 1vq6 , 1vq7 , 1vq8 , 1vq9 , 1vqa , 1vqb , 1vqc , 1vqd , 1vqe , 1vqf , 1vqg , 1vqh , 1vqi , 1vqj , 1vqk , 1vql , 1vqm , 1vqn , 1vqo , 1vqp , 1vs5 , 1vs6 , 1vs7 , 1vs8 , 1w2b , 1wcm , 1wi5 , 1wjj , 1woc , 1wyd , 1x3e , 1x3f , 1x3g , 1x54 , 1x55 , 1x56 , 1x6o , 1x9n , 1xbp , 1xjv , 1xmo , 1xmq , 1xnq , 1xnr , 1xtd , 1y14 , 1y1v , 1y1w , 1y1y , 1y77 , 1yby , 1yha , 1yhb , 1yhq , 1yi2 , 1yij , 1yit , 1yj9 , 1yjn , 1yjw , 1yl3 , 1yl4 , 1z9f , 2a19 , 2a1a , 2aho , 2akw , 2aly , 2amc , 2asb , 2atw , 2avy , 2aw4 , 2aw7 , 2awb , 2b29 , 2b3g , 2b63 , 2b64 , 2b8k , 2b9m , 2b9o , 2ba0 , 2c35 , 2ccz , 2cwp , 2dud , 2e2h , 2e2i , 2e2j , 2e5l , 2es2 , 2f4v , 2f52 , 2gn5 , 2gva , 2gvb , 2h5x , 2hax , 2hgi , 2hgj , 2hgp , 2hgq , 2hgr , 2hgu , 2hhh , 2i0q , 2i2p , 2i2t , 2i2u , 2i2v , 2iy5 , 2j00 , 2j01 , 2j02 , 2j03 , 2ja5 , 2ja6 , 2ja7 , 2ja8 , 2je6 , 2jea , 2nvq , 2nvt , 2nvx , 2nvy , 2nvz , 2nzh , 2nzo , 2oce , 2otj , 2otl , 2pi2 , 2pmz , 2pnh , 2pqa , 2q2t , 2q2u , 2qal , 2qam , 2qan , 2qao , 2qb9 , 2qba , 2qbb , 2qbc , 2qbd , 2qbe , 2qbf , 2qbg , 2qbh , 2qbi , 2qbj , 2qbk , 2qou , 2qov , 2qow , 2qox , 2qoy , 2qoz , 2qp0 , 2qp1 , 2r7z , 2r92 , 2r93 , 2uu9 , 2uua , 2uub , 2uuc , 2uxb , 2uxc , 2uxd , 2v46 , 2v48 , 2vhm , 2vhn , 2vho , 2vhp , 2vqe , 2vqf , 2vum , 2yu9 , 2z4k , 2z4l , 2z4m , 2z4n , 2z6k , 2zjp , 2zjq , 2zjr , 3bzc , 3bzk , 3cf5 , 3cqz , 3d5a , 3d5c , 3df1 , 3df2 , 3df3 , 3df4 , 3mef , 3ull

Taxonomic coverageHelp
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Overlapping InterPro entriesHelp
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IPR012340 Numbers of overlapping proteins Average numbers of overlapping amino acids

Example proteinsHelp
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P04802 Aspartyl-tRNA synthetase, cytoplasmic

P05198 Eukaryotic translation initiation factor 2 subunit 1

P10735 40S ribosomal protein S12, mitochondrial

P34496 Mitochondrial single stranded DNA binding protein 1

Q8K1R3 Polyribonucleotide nucleotidyltransferase 1, mitochondrial

More proteins


Example Proteins Key


InterPro entry accession number/name and structure databases Colour code
IPR020568 Ribosomal protein S5 domain 2-type fold
IPR018111 K Homology, type 1, subgroup
IPR015847 Exoribonuclease, phosphorolytic domain 2
IPR015848 Polynucleotide phosphorylase, phosphorolytic RNA-binding, bacterial/organelle-type
IPR018150 Aminoacyl-tRNA synthetase, class II (D/K/N)-like
IPR000424 Primosome PriB/single-strand DNA-binding
IPR001247 Exoribonuclease, phosphorolytic domain 1
IPR003029 Ribosomal protein S1, RNA binding domain
IPR011488 Eukaryotic translation initiation factor 2, alpha subunit
IPR006032 Ribosomal protein S12/S23
IPR016027 Nucleic acid-binding, OB-fold-like
IPR011344 Single-strand DNA-binding
IPR012340 Nucleic acid-binding, OB-fold
IPR004087 K Homology
IPR004088 K Homology, type 1
IPR002312 Aspartyl-tRNA synthetase, class IIb
IPR005679 Ribosomal protein S12, bacterial-type
IPR012162 Polyribonucleotide nucleotidyltransferase
IPR004523 Aspartyl-tRNA synthetase, class IIb, archea/euk type
IPR006195 Aminoacyl-tRNA synthetase, class II, conserved region
IPR004365 Nucleic acid binding, OB-fold, tRNA/helicase-type
IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N)
ModBase
SWISS-MODEL
PDB Chain
CATH Domain
SCOP Domain

PublicationsHelp
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1. Agrawal V, Kishan KV.
OB-fold: growing bigger with functional consistency.
Curr. Protein Pept. Sci. 4 195-206 2003 [PubMed: 12769718]
http://openurl.ingenta.com/content?genre=article&issn=1389-2037&volume=4&issue=3&spage=195
2. Draper DE, Reynaldo LP.
RNA binding strategies of ribosomal proteins.
Nucleic Acids Res. 27 381-8 1999 [PubMed: 9862955]
http://dx.doi.org/10.1093/nar/27.2.381
3. Ginalski K, Kinch L, Rychlewski L, Grishin NV.
BOF: a novel family of bacterial OB-fold proteins.
FEBS Lett. 567 297-301 2004 [PubMed: 15178340]
http://dx.doi.org/10.1016/j.febslet.2004.04.086

Additional ReadingHelp
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Kurata S, Weixlbaumer A, Ohtsuki T, Shimazaki T, Wada T, Kirino Y, Takai K, Watanabe K, Ramakrishnan V, Suzuki T.
Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding.
J. Biol. Chem. 283 2008 18801-11 [PubMed: 18456657]
http://dx.doi.org/10.1074/jbc.M800233200
Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P.
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
Mol. Cell 30 2008 26-38 [PubMed: 18406324]
http://dx.doi.org/10.1016/j.molcel.2008.01.009
Kaplan CD, Larsson KM, Kornberg RD.
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin.
Mol. Cell 30 2008 547-56 [PubMed: 18538653]
http://dx.doi.org/10.1016/j.molcel.2008.04.023
Hirata A, Klein BJ, Murakami KS.
The X-ray crystal structure of RNA polymerase from Archaea.
Nature 451 2008 851-4 [PubMed: 18235446]
http://dx.doi.org/10.1038/nature06530
Borovinskaya MA, Shoji S, Fredrick K, Cate JH.
Structural basis for hygromycin B inhibition of protein biosynthesis.
RNA 14 2008 1590-9 [PubMed: 18567815]
http://dx.doi.org/10.1261/rna.1076908
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InterPro 23.1