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5  structures 2032  species 0  interactions 5209  sequences 143  architectures

Family: OB_NTP_bind (PF07717)

Summary: Oligonucleotide/oligosaccharide-binding (OB)-fold

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Oligonucleotide/oligosaccharide-binding (OB)-fold Provide feedback

This family is found towards the C-terminus of the DEAD-box helicases (PF00270). In these helicases it is apparently always found in association with PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Q84VZ2. The structure PDB:3i4u adopts an OB-fold. helicases (PF00270). In these helicases it is apparently always found in association with PF04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins [1].

Literature references

  1. Walbott H, Mouffok S, Capeyrou R, Lebaron S, Humbert O, van Tilbeurgh H, Henry Y, Leulliot N;, EMBO J. 2010;29:2194-2204.: Prp43p contains a processive helicase structural architecture with a specific regulatory domain. PUBMED:20512115 EPMC:20512115

  2. Kim T, Pazhoor S, Bao M, Zhang Z, Hanabuchi S, Facchinetti V, Bover L, Plumas J, Chaperot L, Qin J, Liu YJ;, Proc Natl Acad Sci U S A. 2010; [Epub ahead of print]: Aspartate-glutamate-alanine-histidine box motif (DEAH)/RNA helicase A helicases sense microbial DNA in human plasmacytoid dendritic cells. PUBMED:20696886 EPMC:20696886


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011709

This domain is found towards the C terminus of the DEAD-box helicases (INTERPRO). In these helicases it appears to be always found in association with INTERPRO.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan OB (CL0021), which has the following description:

The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. 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 [1].

The clan contains the following 45 members:

BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_NTP_bind OB_RNB OmdA Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(118)
Full
(5209)
Representative proteomes NCBI
(4906)
Meta
(191)
RP15
(873)
RP35
(1456)
RP55
(2200)
RP75
(2747)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(118)
Full
(5209)
Representative proteomes NCBI
(4906)
Meta
(191)
RP15
(873)
RP35
(1456)
RP55
(2200)
RP75
(2747)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(118)
Full
(5209)
Representative proteomes NCBI
(4906)
Meta
(191)
RP15
(873)
RP35
(1456)
RP55
(2200)
RP75
(2747)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Yeats C
Previous IDs: DUF1605;
Type: Domain
Author: Yeats C
Number in seed: 118
Number in full: 5209
Average length of the domain: 134.10 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 12.53 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.5 21.4
Noise cut-off 21.2 21.1
Model length: 114
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Structures

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 OB_NTP_bind domain has been found. There are 5 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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