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4  structures 2408  species 0  interactions 6772  sequences 60  architectures

Family: MPAB_Lcp_cat (PF09995)

Summary: ER-bound oxygenase mpaB/B'/Rubber oxygenase, catalytic domain

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This is the Wikipedia entry entitled "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A Domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF188 and DUF1000. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[1] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[2]

External Links

List of Pfam familes beginning with the letter D, including DUF families

References

  1. ^ Schultz J, Milpetz F, Bork P, Ponting CP (1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. PMC 34487. PMID 9600884. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Jaroszewski L, Li Z, Krishna SS; et al. (2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

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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.

ER-bound oxygenase mpaB/B'/Rubber oxygenase, catalytic domain Provide feedback

This is the catalytic domain found in the endoplasmic reticulum (ER) -bound oxygenases mpaB' (MPAB2) and mpaB (MPAB) from Penicillium roqueforti and Penicillium brevicompactum and in the rubber oxygenase (Lcp) from Streptomyces sp., which contains highly conserved arginine and histidine residues. Structural analysis from Lcp revealed that Arg164, Thr168 and His198 are crucial active site residues [1]. The mpaB and mpaB' are part of the gene cluster that mediates the biosynthesis of mycophenolic acid (MPA) [2]. Lcp (Latex clearing proteins) is a rubber oxygenase that catalyses the extracellular cleavage of poly (cis-1,4-isoprene) [1,3]. This domain is also present in uncharacterised proteins from Mycobacterium sp. and hypothetical proteins, mainly from bacteria and fungi.

Literature references

  1. Ilcu L, Rother W, Birke J, Brausemann A, Einsle O, Jendrossek D;, Sci Rep. 2017;7:6179.: Structural and Functional Analysis of Latex Clearing Protein (Lcp) Provides Insight into the Enzymatic Cleavage of Rubber. PUBMED:28733658 EPMC:28733658

  2. Zhang W, Du L, Qu Z, Zhang X, Li F, Li Z, Qi F, Wang X, Jiang Y, Men P, Sun J, Cao S, Geng C, Qi F, Wan X, Liu C, Li S;, Proc Natl Acad Sci U S A. 2019;116:13305-13310.: Compartmentalized biosynthesis of mycophenolic acid. PUBMED:31209052 EPMC:31209052

  3. Birke J, Rother W, Jendrossek D;, Appl Environ Microbiol. 2015;81:3793-3799.: Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30 Is a b-Type Cytochrome and Differs from Rubber Oxygenase A (RoxA) in Its Biophysical Properties. PUBMED:25819959 EPMC:25819959


This tab holds annotation information from the InterPro database.

InterPro entry IPR018713

This entry represents the catalytic domain found in the endoplasmic reticulum (ER)-bound oxygenases mpaB' (MPAB2) and mpaB (MPAB) from Penicillium roqueforti and Penicillium brevicompactum and in the rubber oxygenase (Lcp) from Streptomyces sp., which contains highly conserved arginine and histidine residues. Structural analysis from Lcp revealed that Arg164, Thr168 and His198 are crucial active site residues [ PUBMED:28733658 ]. The ER-bound oxygenases mpaB and mpaB' are part of the gene cluster that mediates the biosynthesis of mycophenolic acid (MPA) and mediates the oxidative cleavage the C19-C20 double bond in farnesyl-DHMP (FDHMP) to yield FDHMP-3C via a mycophenolic aldehyde intermediate [ PUBMED:31209052 ]. Rubber oxygenase Lcp (Latex clearing proteins) is a rubber oxygenase that catalyses the extracellular cleavage of poly (cis-1,4-isoprene) by Gram-positive rubber degrading bacteria such as Streptomyces sp. K30 [ PUBMED:28733658 , PUBMED:25819959 ]. This domain is also present in uncharacterised proteins from Mycobacterium sp. and hypothetical proteins, mainly from bacteria and fungi.

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 (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
(243)
Full
(6772)
Representative proteomes UniProt
(26078)
RP15
(595)
RP35
(2539)
RP55
(6681)
RP75
(12621)
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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
(243)
Full
(6772)
Representative proteomes UniProt
(26078)
RP15
(595)
RP35
(2539)
RP55
(6681)
RP75
(12621)
Alignment:
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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
(243)
Full
(6772)
Representative proteomes UniProt
(26078)
RP15
(595)
RP35
(2539)
RP55
(6681)
RP75
(12621)
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: COGs (COG3662)
Previous IDs: DUF2236;
Type: Domain
Sequence Ontology: SO:0000417
Author: COGs, Finn RD , Sammut SJ , Chuguransky S
Number in seed: 243
Number in full: 6772
Average length of the domain: 233.3 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 66.89 %

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 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 224
Family (HMM) version: 12
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 MPAB_Lcp_cat domain has been found. There are 4 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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