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24  structures 4462  species 3  interactions 5286  sequences 57  architectures

Family: DNA_ligase_aden (PF01653)

Summary: NAD-dependent DNA ligase adenylation 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.

NAD-dependent DNA ligase adenylation domain Provide feedback

DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism [1].

Literature references

  1. Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW; , EMBO J 2000;19:1119-1129.: Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. PUBMED:10698952 EPMC:10698952

  2. Lim JH, Choi J, Kim W, Ahn BY, Han YS; , Arch Biochem Biophys 2001;388:253-260.: Mutational analyses of Aquifex pyrophilus DNA ligase define essential domains for self-adenylation and DNA binding activity. PUBMED:11368162 EPMC:11368162

  3. Singleton MR, Hakansson K, Timson DJ, Wigley DB; , Structure Fold Des 1999;7:35-42.: Structure of the adenylation domain of an NAD+-dependent DNA ligase. PUBMED:10368271 EPMC:10368271


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013839

DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (EC), the other NAD (EC).

This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [PUBMED:1526462, PUBMED:8390989]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [PUBMED:10368271, PUBMED:10698952].

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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Pfam Clan

This family is a member of clan DNA_ligase (CL0078), which has the following description:

This superfamily contains both ATP-dependent and NAD dependent DNA ligase enzymes. The family also includes mRNA capping enzymes. The members of this clan were shown to be related by sequence in [1].

The clan contains the following 4 members:

DNA_ligase_A_M DNA_ligase_aden mRNA_cap_enzyme RNA_ligase

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
(15)
Full
(5286)
Representative proteomes NCBI
(4137)
Meta
(3767)
RP15
(368)
RP35
(717)
RP55
(925)
RP75
(1089)
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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
(15)
Full
(5286)
Representative proteomes NCBI
(4137)
Meta
(3767)
RP15
(368)
RP35
(717)
RP55
(925)
RP75
(1089)
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
(15)
Full
(5286)
Representative proteomes NCBI
(4137)
Meta
(3767)
RP15
(368)
RP35
(717)
RP55
(925)
RP75
(1089)
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: Pfam-B_1334 (release 4.1)
Previous IDs: DNA_ligase_N;
Type: Domain
Author: Bateman A
Number in seed: 15
Number in full: 5286
Average length of the domain: 299.60 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 46.15 %

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 19.0 19.0
Trusted cut-off 19.0 19.0
Noise cut-off 18.9 18.8
Model length: 315
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 3 interactions for this family. More...

DNA_ligase_aden DNA_ligase_OB DNA_ligase_ZBD

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 DNA_ligase_aden domain has been found. There are 24 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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