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2  structures 472  species 0  interactions 503  sequences 6  architectures

Family: Archease (PF01951)

Summary: Archease protein family (MTH1598/TM1083)

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Archease Edit Wikipedia article

Archease
PDB 1jw3 EBI.jpg
solution structure of methanobacterium thermoautotrophicum protein 1598. ontario centre for structural proteomics target mth1598_1_140; northeast structural genomics target tt6
Identifiers
Symbol Archease
Pfam PF01951
InterPro IPR002804
SCOP 1jw3
SUPERFAMILY 1jw3

In molecular biology, the archease superfamily of proteins are represented in all three domains of life. Archease genes are generally located adjacent to genes encoding proteins involved in DNA or RNA processing and therefore been predicted to be modulators or chaperones involved in DNA or RNA metabolism. Many of the roles of archeases remain to be established experimentally.

The function of one of the archeases from the hyperthermophile Pyrococcus abyssi has been determined. The gene encoding the archease (PAB1946) is located in a bicistronic operon immediately upstream from a second open reading frame (PAB1947), which encodes a tRNA m5C methyltransferase. The methyl transferase catalyses m5C formation at several cytosine's within tRNAs with preference for C49; the pecificity of the methyltransferase reaction being increased by the archease. The archease exists in monomeric and oligomeric states, with only the oligomeric forms able to bind the methyltransferase. Binding prevents aggregation and hinders dimerisation of the methyltransferase-tRNA complex.[1]

The function of this family of archeases as chaperones is supported by structural analysis of the archease from Methanobacterium thermoautotrophicum, which shows homology to heat shock protein 33, a chaperone protein that inhibits the aggregation of partially denatured proteins.[2]

References[edit]

  1. ^ Auxilien S, El Khadali F, Rasmussen A, Douthwaite S, Grosjean H (June 2007). "Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase". J. Biol. Chem. 282 (26): 18711–21. doi:10.1074/jbc.M607459200. PMID 17470432. 
  2. ^ Yee A, Chang X, Pineda-Lucena A, Wu B, Semesi A, Le B, Ramelot T, Lee GM, Bhattacharyya S, Gutierrez P, Denisov A, Lee CH, Cort JR, Kozlov G, Liao J, Finak G, Chen L, Wishart D, Lee W, McIntosh LP, Gehring K, Kennedy MA, Edwards AM, Arrowsmith CH (February 2002). "An NMR approach to structural proteomics". Proc. Natl. Acad. Sci. U.S.A. 99 (4): 1825–30. doi:10.1073/pnas.042684599. PMC 122278. PMID 11854485. 

This article incorporates text from the public domain Pfam and InterPro IPR002804

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.

Archease protein family (MTH1598/TM1083) Provide feedback

This archease family of proteins [1] has two SHS2 domains [2] with one inserted into another. It is predicted to be an enzyme [2]. It is predicted to act as a chaperone in DNA/RNA metabolism [1].

Literature references

  1. Canaves JM; , Proteins. 2004;56:19-27.: Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts. PUBMED:15162483 EPMC:15162483

  2. Anantharaman V, Aravind L;, Proteins. 2004;56:795-807.: The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. PUBMED:15281131 EPMC:15281131

  3. Auxilien S, El Khadali F, Rasmussen A, Douthwaite S, Grosjean H;, J Biol Chem. 2007;282:18711-18721.: Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase. PUBMED:17470432 EPMC:17470432


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR023572

The archease superfamily of proteins are represented in all three domains of life. Archease genes are generally located adjacent to genes encoding proteins involved in DNA or RNA processing and therefore have been predicted to be modulators or chaperones involved in DNA or RNA metabolism. Many of the roles of archeases remain to be established experimentally.

The function of one of the archeases from the hyperthermophile Pyrococcus abyssi has been determined. The gene encoding the archease (PAB1946) is located in a bicistronic operon immediately upstream from a second open reading frame (PAB1947), which encodes a tRNA m5C methyltransferase. The methyl transferase catalyses m5C formation at several cytosine's within tRNAs with preference for C49; the specificity of the methyltransferase reaction being increased by the archease. The archease protects the tRNA (cytosine-5-)-methyltransferase PAB1947 against aggregation and increases its specificity. The archease exists in monomeric and oligomeric states, with only the oligomeric forms able to bind the methyltransferase [PUBMED:17470432].

The function of this family of archeases as chaperones is supported by structural analysis of SWISSPROT from Methanobacterium thermoautotrophicum, which shows homology to heat shock protein 33, which is a chaperone protein that inhibits the aggregation of partially denatured proteins [PUBMED:11854485].

Structurally, the archeases are composed of a single three layer beta-alpha-beta sandwich domain similar to those found in other chaperones.

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 SHS2 (CL0319), which contains the following 7 members:

Archease Cass2 Dodecin GyrI-like SHS2_FTSA SHS2_Rpb7-N SOUL

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
(96)
Full
(503)
Representative proteomes NCBI
(485)
Meta
(93)
RP15
(104)
RP35
(172)
RP55
(233)
RP75
(280)
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  Seed
(96)
Full
(503)
Representative proteomes NCBI
(485)
Meta
(93)
RP15
(104)
RP35
(172)
RP55
(233)
RP75
(280)
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
(96)
Full
(503)
Representative proteomes NCBI
(485)
Meta
(93)
RP15
(104)
RP35
(172)
RP55
(233)
RP75
(280)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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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: Enright A
Previous IDs: DUF101;
Type: Domain
Author: Enright A, Ouzounis C, Bateman A, Anantharaman V
Number in seed: 96
Number in full: 503
Average length of the domain: 134.80 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 85.80 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 41.1 41.1
Noise cut-off 24.6 24.6
Model length: 137
Family (HMM) version: 11
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 Archease domain has been found. There are 2 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 seqence.

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