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83  structures 4347  species 2  interactions 7730  sequences 22  architectures

Family: Dala_Dala_lig_N (PF01820)

Summary: D-ala D-ala ligase N-terminus

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "D-alanine-D-alanine ligase". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

D-ala D-ala ligase N-terminus Provide feedback

This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding [2]. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [3].

Literature references

  1. Fan C, Park IS, Walsh CT, Knox JR; , Biochemistry 1997;36:2531-2538.: D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. PUBMED:9054558 EPMC:9054558

  2. Roper DI, Huyton T, Vagin A, Dodson G; , Proc Natl Acad Sci U S A 2000;97:8921-8925.: The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA). PUBMED:10908650 EPMC:10908650

  3. Feng Z, Barletta RG; , Antimicrob Agents Chemother 2003;47:283-291.: Roles of Mycobacterium smegmatis D-alanine:D-alanine ligase and D-alanine racemase in the mechanisms of action of and resistance to the peptidoglycan inhibitor D-cycloserine. PUBMED:12499203 EPMC:12499203


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011127

This entry represents the N-terminal region of the D-alanine--D-alanine ligase enzyme (EC) which is thought to be involved in substrate binding [PUBMED:10908650]. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [PUBMED:9054558].

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 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
(176)
Full
(7730)
Representative proteomes NCBI
(5359)
Meta
(3003)
RP15
(540)
RP35
(1043)
RP55
(1317)
RP75
(1553)
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Format an alignment

  Seed
(176)
Full
(7730)
Representative proteomes NCBI
(5359)
Meta
(3003)
RP15
(540)
RP35
(1043)
RP55
(1317)
RP75
(1553)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(176)
Full
(7730)
Representative proteomes NCBI
(5359)
Meta
(3003)
RP15
(540)
RP35
(1043)
RP55
(1317)
RP75
(1553)
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: PSI-BLAST 2dln
Previous IDs: Dala_Dala_ligas;
Type: Family
Author: Bateman A, Moxon SJ
Number in seed: 176
Number in full: 7730
Average length of the domain: 82.10 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 32.44 %

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 21.6 21.6
Trusted cut-off 23.0 21.6
Noise cut-off 21.3 21.5
Model length: 117
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Dala_Dala_lig_N Dala_Dala_lig_C

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 Dala_Dala_lig_N domain has been found. There are 83 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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