Summary: Mur ligase middle domain
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Mur ligase middle domain Provide feedback
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Literature references
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Bertrand JA, Auger G, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O; , EMBO J 1997;16:3416-3425.: Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. PUBMED:9218784 EPMC:9218784
This tab holds annotation information from the InterPro database.
InterPro entry IPR013221
The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:
- (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc).
- (2) addition of a short polypeptide chain to the UDPMurNAc.
- (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.
Stage two involves four key Mur ligase enzymes: MurC (EC) [PUBMED:17139082], MurD (EC) [PUBMED:17427948], MurE (EC) [PUBMED:16595662] and MurF (EC) [PUBMED:16322581]. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales [PUBMED:16934839].
This entry represents the central domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [PUBMED:9652408].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | ATP binding (GO:0005524) |
Biological process | biosynthetic process (GO:0009058) |
Domain organisation
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Alignments
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Seed (55) |
Full (41007) |
Representative proteomes | UniProt (202841) |
NCBI (288137) |
Meta (10798) |
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RP15 (5213) |
RP35 (19747) |
RP55 (41204) |
RP75 (71682) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (55) |
Full (41007) |
Representative proteomes | UniProt (202841) |
NCBI (288137) |
Meta (10798) |
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RP15 (5213) |
RP35 (19747) |
RP55 (41204) |
RP75 (71682) |
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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.
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Trees
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Curation and family details
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Curation
Seed source: | Pfam-B_26 (release 17.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 55 |
Number in full: | 41007 |
Average length of the domain: | 191.70 aa |
Average identity of full alignment: | 20 % |
Average coverage of the sequence by the domain: | 39.66 % |
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: | 200 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 5 interactions for this family. More...
Mur_ligase_M Mur_ligase_C Mur_ligase_C Mur_ligase Mur_ligaseStructures
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 Mur_ligase_M domain has been found. There are 103 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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