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InterPro: IPR016027 Nucleic acid-binding, OB-fold-like

Protein matches Help

UniProtKB

Matches:

58576 proteins

Overview:	sorted by AC,	sorted by name,	of known structure,	proteins with splice variants
Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR016027 NA-bd_OB-fold-like

Type

Domain

Signatures Help

Database	ID	Name	Proteins
SuperFamily	SSF50249	Nucleic_acid_OB	58576
Signatures in BioMart

InterPro Relationships Help

Children

IPR012339 Phage single-stranded DNA-binding protein, Gene 32 protein core
IPR012340 Nucleic acid-binding, OB-fold

Found in

IPR000110 Ribosomal protein S1
IPR001566 23S rRNA methyltransferase/RumA
IPR001884 Translation elongation factor, IF5A
IPR002313 Lysyl-tRNA synthetase, class II
IPR003750 Protein of unknown function DUF171
IPR004523 Aspartyl-tRNA synthetase, class IIb, archea/euk type
IPR004524 Aspartyl-tRNA synthetase, class IIb, bacterial/mitochondrial type
IPR004609 DNA helicase, ATP-dependent, RecG
IPR004665 Transcription termination factor Rho
IPR004881 GTPase EngC
IPR006308 DNA polymerase III, alpha subunit, Gram-positive type
IPR010874 Telomere-binding beta subunit
IPR011370 DNA recombination and repair protein, BRCA2
IPR011768 Translation elongation factor P
IPR011897 Translation elongation factor P-like, YeiP
IPR012162 Polyribonucleotide nucleotidyltransferase
IPR014464 Predicted nucleic acid binding protein, YitL type
IPR015525 Breast cancer type 2 susceptibility protein
IPR016798 Uncharacterised conserved protein UCP021980, OB-fold
IPR017074 mRNA capping enzyme, bifunctional
IPR017084 RNA editing complex, subunit MP18
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
IPR020873 3'-5' exoribonuclease YhaM
IPR020923 DNA ligase B

Contains

IPR002792 Deoxyribonuclease/rho motif-related TRAM
IPR003029 Ribosomal protein S1, RNA binding domain
IPR003871 Protein of unknown function DUF223, Arabidopsis thaliana
IPR013852 Translation elongation factor P/YeiP, conserved site
IPR015187 BRCA2, oligonucleotide/oligosaccharide-binding 1
IPR015188 BRCA2, oligonucleotide/oligosaccharide-binding 3
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

Entry Details in BioMart

Abstract

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].

Structural links Help

PDB - click here

SCOP: a.171.1.1 , a.60.14.1 , b.40.4.1 , b.40.4.10 , b.40.4.11 , b.40.4.12 , b.40.4.2 , b.40.4.3 , b.40.4.4 , b.40.4.5 , b.40.4.6 , b.40.4.7 , b.40.4.8 , b.40.4.9 , b.84.4.2 , c.116.1.2 , c.26.1.1 , d.142.2.2 , i.1.1.1 , i.1.1.2 , i.8.1.1

CATH: 1.10.150.190 , 2.20.25.10 , 2.20.28.10 , 2.30.30.30 , 2.40.200.10 , 2.40.50.140 , 3.30.1490.120 , 3.30.1490.70 , 3.30.1640.10 , 3.30.300.20 , 3.30.930.10 , 3.40.1280.10 , 3.90.198.10 , 4.10.87.10

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR016027

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O55236 mRNA-capping enzyme

O60942 mRNA-capping enzyme

P04802 Aspartyl-tRNA synthetase, cytoplasmic

P10735 40S ribosomal protein S12, mitochondrial

P34496 Mitochondrial single stranded DNA binding protein 1

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR013846	mRNA capping enzyme, C-terminal
IPR017074	mRNA capping enzyme, bifunctional
IPR000387	Dual-specific/protein-tyrosine phosphatase, conserved region
IPR006032	Ribosomal protein S12/S23
IPR011344	Single-strand DNA-binding
IPR016027	Nucleic acid-binding, OB-fold-like
IPR016130	Protein-tyrosine phosphatase, active site
IPR000340	Dual specificity phosphatase, catalytic domain
IPR012340	Nucleic acid-binding, OB-fold
IPR005679	Ribosomal protein S12, bacterial-type
IPR002312	Aspartyl-tRNA synthetase, class IIb
IPR000424	Primosome PriB/single-strand DNA-binding
IPR018150	Aminoacyl-tRNA synthetase, class II (D/K/N)-like
IPR004523	Aspartyl-tRNA synthetase, class IIb, archea/euk type
IPR001339	mRNA capping enzyme
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)
	PDB Chain
	ModBase
	CATH Domain
	SWISS-MODEL
	SCOP Domain

Publications Open in usermanual
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 Reading Open in usermanual
	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
	Brueckner F, Cramer P. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat. Struct. Mol. Biol. 15 2008 811-8 [PubMed: 18552824] http://dx.doi.org/10.1038/nsmb.1458
	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
	Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. J. Mol. Biol. 377 2008 1460-73 [PubMed: 18321528] http://dx.doi.org/10.1016/j.jmb.2008.01.096
	Bingel-Erlenmeyer R, Kohler R, Kramer G, Sandikci A, Antolic S, Maier T, Schaffitzel C, Wiedmann B, Bukau B, Ban N. A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing. Nature 452 2008 108-11 [PubMed: 18288106] http://dx.doi.org/10.1038/nature06683

InterPro 23.1