Summary: D-ala D-ala ligase C-terminus
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D-ala D-ala ligase C-terminus Provide feedback
This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. 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
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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
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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
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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
Internal database links
SCOOP: | ATP-grasp ATP-grasp_2 ATP-grasp_3 ATP-grasp_4 ATP-grasp_5 ATPgrasp_ST ATPgrasp_Ter ATPgrasp_YheCD CPSase_L_D2 DUF3182 GARS_A GSH-S_ATP R2K_2 R2K_3 RimK Synapsin_C TTL |
Similarity to PfamA using HHSearch: | GARS_A ATP-grasp ATP-grasp_3 CPSase_L_D2 RimK ATP-grasp_4 ATPgrasp_ST ATPgrasp_YheCD |
External database links
HOMSTRAD: | Dala_Dala_ligas Dala_Dala_ligas_C Dala_Dala_ligas_N |
SCOP: | 2dln |
This tab holds annotation information from the InterPro database.
InterPro entry IPR011095
This entry represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC. 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:12499203].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | D-alanine-D-alanine ligase activity (GO:0008716) |
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 ATP-grasp (CL0179), which has the following description:
The ATP-grasp domain is found in a wide variety of carboxylate-amine/thiol ligases [1]. It is composed of two subdomains, with ATP being bound in the cleft between the two.
The clan contains the following 26 members:
ATP-grasp ATP-grasp_2 ATP-grasp_3 ATP-grasp_4 ATP-grasp_5 ATP-grasp_6 ATPgrasp_ST ATPgrasp_Ter ATPgrasp_TupA ATPgrasp_YheCD CP_ATPgrasp_1 CP_ATPgrasp_2 CPSase_L_D2 D123 Dala_Dala_lig_C DUF1297 GARS_A GSH-S_ATP GSP_synth Ins134_P3_kin PPDK_N R2K_2 R2K_3 RimK Synapsin_C TTLAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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 (13) |
Full (9874) |
Representative proteomes | UniProt (50748) |
NCBI (281935) |
Meta (7793) |
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RP15 (1361) |
RP35 (4835) |
RP55 (9788) |
RP75 (16953) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (13) |
Full (9874) |
Representative proteomes | UniProt (50748) |
NCBI (281935) |
Meta (7793) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1361) |
RP35 (4835) |
RP55 (9788) |
RP75 (16953) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | PSI-BLAST 2dln |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 13 |
Number in full: | 9874 |
Average length of the domain: | 193.10 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 54.81 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 204 | ||||||||||||
Family (HMM) version: | 14 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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_C domain has been found. There are 118 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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