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148  structures 7368  species 0  interactions 11914  sequences 88  architectures

Family: Dala_Dala_lig_C (PF07478)

Summary: D-ala D-ala ligase C-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...

D-alanine-D-alanine ligase Edit Wikipedia article

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

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

D-alanine—D-alanine ligase Edit Wikipedia article

D-alanine—D-alanine ligase
Identifiers
EC no.6.3.2.4
CAS no.9023-63-6
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
D-ala D-ala ligase N-terminus
PDB 1iow EBI.jpg
complex of y216f d-ala:d-ala ligase with adp and a phosphoryl phosphinate
Identifiers
SymbolDala_Dala_lig_N
PfamPF01820
InterProIPR011127
SCOP22dln / SCOPe / SUPFAM
D-ala D-ala ligase C-terminus
PDB 1iow EBI.jpg
complex of y216f d-ala:d-ala ligase with adp and a phosphoryl phosphinate
Identifiers
SymbolDala_Dala_lig_C
PfamPF07478
Pfam clanCL0179
InterProIPR011095
SCOP22dln / SCOPe / SUPFAM

In enzymology, a D-alanine—D-alanine ligase (EC 6.3.2.4) is an enzyme that catalyzes the chemical reaction

ATP + 2 D-alanine ADP + phosphate + D-alanyl-D-alanine

Thus, the two substrates of this enzyme are ATP and D-alanine, whereas its 3 products are ADP, phosphate, and D-alanyl-D-alanine.

This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The systematic name of this enzyme class is D-alanine:D-alanine ligase (ADP-forming). Other names in common use include alanine:alanine ligase (ADP-forming), and alanylalanine synthetase. This enzyme participates in d-alanine metabolism and peptidoglycan biosynthesis. Phosphinate and D-cycloserine are known to inhibit this enzyme.

The N-terminal region of the D-alanine—D-alanine ligase is thought to be involved in substrate binding, while the C-terminus is thought to be a catalytic domain.[1]

Structural studies

As of late 2007, 8 structures have been solved for this class of enzymes, with PDB accession codes 1EHI, 1IOV, 1IOW, 2DLN, 2FB9, 2I80, 2I87, and 2I8C.

References

Further reading

This article incorporates text from the public domain Pfam and InterPro: IPR011127


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 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

  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


Internal database links

External database links

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.

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 TTL

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...

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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
(12)
Full
(11914)
Representative proteomes UniProt
(63017)
RP15
(1711)
RP35
(5996)
RP55
(12171)
RP75
(20947)
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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
(12)
Full
(11914)
Representative proteomes UniProt
(63017)
RP15
(1711)
RP35
(5996)
RP55
(12171)
RP75
(20947)
Alignment:
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Order:
Sequence:
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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
(12)
Full
(11914)
Representative proteomes UniProt
(63017)
RP15
(1711)
RP35
(5996)
RP55
(12171)
RP75
(20947)
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: PSI-BLAST 2dln
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Moxon SJ
Number in seed: 12
Number in full: 11914
Average length of the domain: 193.40 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 54.65 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 204
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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 Dala_Dala_lig_C domain has been found. There are 148 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
A0A1D6F4U5 View 3D Structure Click here
A0A1I9LPE3 View 3D Structure Click here
A0JXX3 View 3D Structure Click here
A0KKW8 View 3D Structure Click here
A0L5M8 View 3D Structure Click here
A0LQR5 View 3D Structure Click here
A0Q323 View 3D Structure Click here
A0QUZ7 View 3D Structure Click here
A0ZZT4 View 3D Structure Click here
A1AU58 View 3D Structure Click here
A1AX29 View 3D Structure Click here
A1BH06 View 3D Structure Click here
A1K3U8 View 3D Structure Click here
A1R7J5 View 3D Structure Click here
A1S6V2 View 3D Structure Click here
A1T708 View 3D Structure Click here
A1TKD3 View 3D Structure Click here
A1UEB6 View 3D Structure Click here
A1UTC2 View 3D Structure Click here
A1VST4 View 3D Structure Click here
A1WC04 View 3D Structure Click here
A1WRL3 View 3D Structure Click here
A1WYU0 View 3D Structure Click here
A2SCY7 View 3D Structure Click here
A3CLS3 View 3D Structure Click here
A3DGS7 View 3D Structure Click here
A3MY92 View 3D Structure Click here
A3PEE0 View 3D Structure Click here
A3QEV1 View 3D Structure Click here
A4G8T6 View 3D Structure Click here
A4I1M6 View 3D Structure Click here
A4I2H5 View 3D Structure Click here
A4J5G8 View 3D Structure Click here
A4SE28 View 3D Structure Click here
A4VII0 View 3D Structure Click here
A4XQS6 View 3D Structure Click here
A4YRU4 View 3D Structure Click here
A5D2F9 View 3D Structure Click here
A5EY21 View 3D Structure Click here
A5FUL3 View 3D Structure Click here