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266  structures 8805  species 0  interactions 36374  sequences 309  architectures

Family: tRNA_anti-codon (PF01336)

Summary: OB-fold nucleic acid binding domain

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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.

OB-fold nucleic acid binding domain Provide feedback

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 hetero-trimeric 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

  1. 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 EPMC:2047877

  2. 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 EPMC:7760808

  3. 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 EPMC:8990123

  4. 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 EPMC:10829230


Internal database links

External database links

This tab holds annotation information from the InterPro database.

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 INTERPRO ). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC . 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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite 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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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(542)
Full
(36374)
Representative proteomes UniProt
(154097)
RP15
(5679)
RP35
(17885)
RP55
(34747)
RP75
(56378)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(542)
Full
(36374)
Representative proteomes UniProt
(154097)
RP15
(5679)
RP35
(17885)
RP55
(34747)
RP75
(56378)
Alignment:
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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
(542)
Full
(36374)
Representative proteomes UniProt
(154097)
RP15
(5679)
RP35
(17885)
RP55
(34747)
RP75
(56378)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: [4]
Previous IDs: Aspartyl_tRNA_N; tRNA_anti;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Mian N , Finn RD
Number in seed: 542
Number in full: 36374
Average length of the domain: 81.60 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 13.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 76
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 tRNA_anti-codon domain has been found. There are 266 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2K7D7 View 3D Structure Click here
A0A0P0VEM7 View 3D Structure Click here
A0A0P0WGZ9 View 3D Structure Click here
A0A0R0F936 View 3D Structure Click here
A0A0R0IKR4 View 3D Structure Click here
A0A0R0K9M1 View 3D Structure Click here
A0A0R4IAS3 View 3D Structure Click here
A0A1D6EVR1 View 3D Structure Click here
A0A1D6FGX9 View 3D Structure Click here
A0A1D6FII0 View 3D Structure Click here
A0A1D6GM16 View 3D Structure Click here
A0A1D6IBP5 View 3D Structure Click here
A0A1D6KWD0 View 3D Structure Click here
A0A1D6LAQ0 View 3D Structure Click here
A0A1D8PD81 View 3D Structure Click here
A0A1D8PQY7 View 3D Structure Click here
A4HWC4 View 3D Structure Click here
A4HWC8 View 3D Structure Click here
A4I3Q8 View 3D Structure Click here
A4I508 View 3D Structure Click here
A4I574 View 3D Structure Click here
A4IA13 View 3D Structure Click here
B4FWF2 View 3D Structure Click here
B6U4N8 View 3D Structure Click here
B8A5D3 View 3D Structure Click here
B8JKF4 View 3D Structure Click here
C0HES8 View 3D Structure Click here
C0P3D1 View 3D Structure Click here
C0P4T5 View 3D Structure Click here
C0PFF9 View 3D Structure Click here
E9AGV6 View 3D Structure Click here
E9QFP3 View 3D Structure Click here
F1LPV0 View 3D Structure Click here
F1R246 View 3D Structure Click here
F4JJT9 View 3D Structure Click here
F4JSG3 View 3D Structure Click here
I1JMN9 View 3D Structure Click here
I1JZI1 View 3D Structure Click here
I1K5N2 View 3D Structure Click here
I1K622 View 3D Structure Click here
I1KPU2 View 3D Structure Click here
I1KU98 View 3D Structure Click here
I1L9B1 View 3D Structure Click here
I1LZI3 View 3D Structure Click here
I1M9R5 View 3D Structure Click here
I1MHC1 View 3D Structure Click here
I1MT69 View 3D Structure Click here
I1MWJ6 View 3D Structure Click here
I1MX58 View 3D Structure Click here
K7LF83 View 3D Structure Click here
K7LWV0 View 3D Structure Click here
K7MJN5 View 3D Structure Click here
M9PDL2 View 3D Structure Click here
O16689 View 3D Structure Click here
O43776 View 3D Structure Click here
O48593 View 3D Structure Click here
O74858 View 3D Structure Click here
O94242 View 3D Structure Click here
O94567 View 3D Structure Click here
O96198 View 3D Structure Click here
P04802 View 3D Structure Click here
P0A8M0 View 3D Structure Click here
P0A8N3 View 3D Structure Click here
P0A8N5 View 3D Structure Click here
P10443 View 3D Structure Click here
P14868 View 3D Structure Click here
P15178 View 3D Structure Click here
P15179 View 3D Structure Click here
P15180 View 3D Structure Click here
P21889 View 3D Structure Click here
P22336 View 3D Structure Click here
P25345 View 3D Structure Click here
P26754 View 3D Structure Click here
P27694 View 3D Structure Click here
P32048 View 3D Structure Click here
P38707 View 3D Structure Click here
P90831 View 3D Structure Click here
P9WFU7 View 3D Structure Click here
P9WFU9 View 3D Structure Click here
P9WFW3 View 3D Structure Click here
Q03577 View 3D Structure Click here
Q10KX7 View 3D Structure Click here
Q10Q08 View 3D Structure Click here
Q15046 View 3D Structure Click here
Q19537 View 3D Structure Click here
Q19722 View 3D Structure Click here
Q22099 View 3D Structure Click here
Q24492 View 3D Structure Click here
Q2FXU5 View 3D Structure Click here
Q2FYH6 View 3D Structure Click here
Q2G0Q3 View 3D Structure Click here
Q2G2T1 View 3D Structure Click here
Q3KRD0 View 3D Structure Click here
Q3SWT1 View 3D Structure Click here
Q4CNC1 View 3D Structure Click here
Q4CRU7 View 3D Structure Click here
Q4CU45 View 3D Structure Click here
Q4CZG6 View 3D Structure Click here
Q4D7V3 View 3D Structure Click here
Q4DEP8 View 3D Structure Click here
Q4DLP1 View 3D Structure Click here
Q4DQH8 View 3D Structure Click here
Q4DQV9 View 3D Structure Click here
Q4DTR8 View 3D Structure Click here
Q4DXC9 View 3D Structure Click here
Q4E595 View 3D Structure Click here
Q54TY4 View 3D Structure Click here
Q554D9 View 3D Structure Click here
Q55C99 View 3D Structure Click here
Q55FI3 View 3D Structure Click here
Q58228 View 3D Structure Click here
Q58495 View 3D Structure Click here
Q58559 View 3D Structure Click here
Q58559 View 3D Structure Click here
Q58559 View 3D Structure Click here
Q58950 View 3D Structure Click here
Q59R18 View 3D Structure Click here
Q59UF7 View 3D Structure Click here
Q59Z33 View 3D Structure Click here
Q5ACX4 View 3D Structure Click here
Q5ADU2 View 3D Structure Click here
Q5XIM7 View 3D Structure Click here
Q65XV7 View 3D Structure Click here
Q6AYD2 View 3D Structure Click here
Q6DHE6 View 3D Structure Click here
Q6F2U9 View 3D Structure Click here
Q6H7J5 View 3D Structure Click here
Q6K1T2 View 3D Structure Click here
Q6NY74 View 3D Structure Click here
Q6PI48 View 3D Structure Click here
Q6YZ49 View 3D Structure Click here
Q6ZHC3 View 3D Structure Click here
Q7JZR5 View 3D Structure Click here
Q7K0E6 View 3D Structure Click here
Q7TP21 View 3D Structure Click here
Q8BGV0 View 3D Structure Click here
Q8BIP0 View 3D Structure Click here
Q8BP47 View 3D Structure Click here
Q8H104 View 3D Structure Click here
Q8I2B1 View 3D Structure Click here
Q8I408 View 3D Structure Click here
Q8IDJ8 View 3D Structure Click here
Q8II42 View 3D Structure Click here
Q8IIN9 View 3D Structure Click here
Q8K2X3 View 3D Structure Click here
Q8LFJ8 View 3D Structure Click here
Q8R2Y9 View 3D Structure Click here
Q8VEE4 View 3D Structure Click here
Q922B2 View 3D Structure Click here
Q92372 View 3D Structure Click here
Q92373 View 3D Structure Click here
Q93WM3 View 3D Structure Click here
Q96I59 View 3D Structure Click here
Q99MN1 View 3D Structure Click here
Q9BQ15 View 3D Structure Click here
Q9F1K0 View 3D Structure Click here
Q9FHJ6 View 3D Structure Click here
Q9FME0 View 3D Structure Click here
Q9H668 View 3D Structure Click here
Q9LJE2 View 3D Structure Click here
Q9LMK5 View 3D Structure Click here
Q9M084 View 3D Structure Click here
Q9P6I0 View 3D Structure Click here
Q9SD82 View 3D Structure Click here
Q9SKI4 View 3D Structure Click here
Q9SSK1 View 3D Structure Click here
Q9SW96 View 3D Structure Click here
Q9U0J0 View 3D Structure Click here
Q9UUE6 View 3D Structure Click here
Q9V434 View 3D Structure Click here
Q9W327 View 3D Structure Click here
Q9ZPI1 View 3D Structure Click here
Q9ZQ19 View 3D Structure Click here