Summary

OB-fold nucleic acid binding domain

This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.

Literature references

Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D; , Science 1991;252:1682-1689.: Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). PUBMED:2047877
Keshav KF, Chen C, Dutta A; , Mol Cell Biol 1995;15:3119-3128.: Rpa4, a homolog of the 34-kilodalton subunit of the replication protein A complex. PUBMED:7760808
Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L; , Nature 1997;385:176-181.: Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. PUBMED:8990123
Koonin EV, Wolf YI, Aravind L; , Adv Protein Chem 2000;54:245-275.: Protein fold recognition using sequence profiles and its application in structural genomics. PUBMED:10829230

InterPro entry IPR004365

The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates.

This entry contains OB-fold domains that bind to nucleic acids PUBMED:10829230. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See ). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule . This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family PUBMED:7760808, PUBMED:8990123. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.

Clan

This family is a member of clan OB (CL0021), which contains the following 32 members:

BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_RNB Phage_DNA_bind Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosomal_L2 Ribosomal_S12 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 SSB Stn1 Telo_bind TOBE TOBE_2 TRAM tRNA_anti tRNA_bind

Gene Ontology

Molecular function

nucleic acid binding (GO:0003676)

External database links

HOMSTRAD:	asprs
PANDIT:	PF01336
SCOP:	1asy
SYSTERS:	tRNA_anti

Domain organisation

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

Loading domain graphics...

Alignments

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (642) Full (9423) NCBI (13546) Metagenomics (6514)
Viewer:

Formatting options

Alignment:	Seed (642) Full (9423)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

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

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (642) Full (9423) NCBI (13546) Metagenomics (6514)
Full length sequences	Full-sequences (9423)

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 HMMER2.

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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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

Seed source:

[4]

Previous IDs:

Aspartyl_tRNA_N;

Type:

Domain

Author:

Bateman A, Mian N, Finn RD

Number in seed:

642

Number in full:

9423

Average length of the domain:

79.90 aa

Average identity of full alignment:

19 %

Average coverage of the sequence by the domain:

12.71 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.3	20.3
Trusted cut-off	20.3	20.3
Noise cut-off	20.2	20.2

Model length:

76

Family (HMM) version:

18

Download:

download the raw HMM for this family

Species distribution

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

Loading...

Interactions

There are 4 interactions for this family. More...

Rep_fac-A_3 tRNA-synt_2 Rep_fac-A_C DNA_pol3_alpha

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 tRNA_anti domain has been found.

Loading structure mapping...

Family: tRNA_anti (PF01336)

Jump to...