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27  structures 3232  species 0  interactions 13275  sequences 37  architectures

Family: LytR_cpsA_psr (PF03816)

Summary: LytR_cpsA_psr family

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This is the Wikipedia entry entitled "LCP family". More...

LCP family Edit Wikipedia article

Cell envelope-related transcriptional attenuator domain (TagU catalytic domain)
Identifiers
SymbolLytR_cpsA_psr
PfamPF03816
InterProIPR004474
CATH3tflA02
UniProt family
Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagU
Identifiers
SymbolTagU
InterProIPR023734
describes same family; this is the full-length protein
LytR/CpsA/Psr, C-terminal domain
Identifiers
SymbolLytR_C
PfamPF13399
InterProIPR027381

The LCP family or TagU family of proteins is a conserved family of proteins that are involved in the attachment of wall teichoic acid (WTA) molecules to gram-positive cell walls. It was initially thought as the LytR (lytic repressor) component of a LytABC operon encoding autolysins,[1] but the mechanism of regulation was later realized to be the production of WTA molecules and renamed TagU.[2]

The "LCP" acronym derives from three proteins initially identified to contain this domain, LytR (now TagU, Q02115), cpsA ("Capsular polysaccharide expression regulator"), and psr ("PBP 5 synthesis repressor"). These proteins were mistaken as transcriptional regulators via different reasons, but all three of them are now known to be TauU-like enzymes.[3][4]

Typical LCP proteins are made up of an N-terminal transmembrane domain (for anchoring), an optional, non-conserved accessory domain (CATH 3tflA01), a core catalytic domain, and sometimes a C-terminal domain for which the structure is unknown. The core LCP domain is a magnesium-dependent enzyme.[2]

  1. ^ Lazarevic, V.; Margot, P.; Soldo, B.; Karamata, D. (1 September 1992). "Sequencing and analysis of the Bacillus subtilis lytRABC divergon: A regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier". Journal of General Microbiology. 138 (9): 1949–1961. doi:10.1099/00221287-138-9-1949.
  2. ^ a b Kawai, Yoshikazu; Marles-Wright, Jon; Cleverley, Robert M; Emmins, Robyn; Ishikawa, Shu; Kuwano, Masayoshi; Heinz, Nadja; Bui, Nhat Khai; Hoyland, Christopher N; Ogasawara, Naotake; Lewis, Richard J; Vollmer, Waldemar; Daniel, Richard A; Errington, Jeff (14 December 2011). "A widespread family of bacterial cell wall assembly proteins". The EMBO Journal. 30 (24): 4931–4941. doi:10.1038/emboj.2011.358. PMC 3243631. PMID 21964069.
  3. ^ Wang, Qinglan; Zhu, Lin; Jones, Victoria; Wang, Chuan; Hua, Yifei; Shi, Xujun; Feng, Xia; Jackson, Mary; Niu, Chen; Gao, Qian; Ehrt, S. (July 2015). "CpsA, a LytR-CpsA-Psr Family Protein in Mycobacterium marinum, Is Required for Cell Wall Integrity and Virulence". Infection and Immunity. 83 (7): 2844–2854. doi:10.1128/IAI.03081-14. PMID 25939506.
  4. ^ Maréchal, Maxime; Amoroso, Ana; Morlot, Cécile; Vernet, Thierry; Coyette, Jacques; Joris, Bernard (12 October 2016). "Enterococcus hirae LcpA (Psr), a new peptidoglycan-binding protein localized at the division site". BMC Microbiology. 16 (1). doi:10.1186/s12866-016-0844-y.

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.

LytR_cpsA_psr family Provide feedback

The entry represents a domain found in a number of LCP (LytR-Cps2A-Psr) family proteins. LCP family is also known as TagU family. LCP family proteins have been reported to be required for the synthesis of anionic cell wall polymers [1].

Literature references

  1. Kawai Y, Marles-Wright J, Cleverley RM, Emmins R, Ishikawa S, Kuwano M, Heinz N, Bui NK, Hoyland CN, Ogasawara N, Lewis RJ, Vollmer W, Daniel RA, Errington J;, EMBO J. 2011;30:4931-4941.: A widespread family of bacterial cell wall assembly proteins. PUBMED:21964069 EPMC:21964069


This tab holds annotation information from the InterPro database.

InterPro entry IPR004474

This entry describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is protein psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. These proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor.

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

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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
(32)
Full
(13275)
Representative proteomes UniProt
(57225)
RP15
(1200)
RP35
(6245)
RP55
(14289)
RP75
(24245)
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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
(32)
Full
(13275)
Representative proteomes UniProt
(57225)
RP15
(1200)
RP35
(6245)
RP55
(14289)
RP75
(24245)
Alignment:
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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
(32)
Full
(13275)
Representative proteomes UniProt
(57225)
RP15
(1200)
RP35
(6245)
RP55
(14289)
RP75
(24245)
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: TIGRFAMs
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: TIGRFAMs, Griffiths-Jones SR
Number in seed: 32
Number in full: 13275
Average length of the domain: 157.1 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 37.09 %

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 24.6 24.6
Trusted cut-off 24.6 24.6
Noise cut-off 24.5 24.5
Model length: 152
Family (HMM) version: 17
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 LytR_cpsA_psr domain has been found. There are 27 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