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52  structures 1792  species 4  interactions 3260  sequences 46  architectures

Family: RMMBL (PF07521)

Summary: Zn-dependent metallo-hydrolase RNA specificity domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Zn-dependent metallo-hydrolase RNA specificity domain Provide feedback

The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in PF00753 and are common to all metallo-beta-lactamases. This, the fifth motif [1] appears to be specific to Zn-dependent metallohydrolases such as ribonuclease J 2 [4] which are involved in the processing of mRNA [2,3]. This domain adds essential structural elements to the CASP-domain and is unique to RNA/DNA-processing nucleases, showing that they are pre-mRNA 3′-end-processing endonucleases [2,3,4].

Literature references

  1. Callebaut I, Moshous D, Mornon JP, de Villartay JP; , Nucleic Acids Res 2002;30:3592-3601.: Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. PUBMED:12177301 EPMC:12177301

  2. Mandel CR, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley JL, Tong L; , Nature. 2006;444:953-956.: Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. PUBMED:17128255 EPMC:17128255

  3. Nishida Y, Ishikawa H, Baba S, Nakagawa N, Kuramitsu S, Masui R;, Proteins. 2010;78:2395-2398.: Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii. PUBMED:20544974 EPMC:20544974

  4. Roux CM, DeMuth JP, Dunman PM;, J Bacteriol. 2011;193:5520-5526.: Characterization of components of the Staphylococcus aureus mRNA degradosome holoenzyme-like complex. PUBMED:21764917 EPMC:21764917


This tab holds annotation information from the InterPro database.

InterPro entry IPR011108

The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism [PUBMED:12177301].

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 RMMBL_DRMBL (CL0398), which has the following description:

This clan contains the fifth motif found in RNA and DNA metabolising metallo-beta-lactamases. The fifth motif appears to be specific to function [1].

The clan contains the following 2 members:

DRMBL RMMBL

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(99)
Full
(3260)
Representative proteomes UniProt
(12838)
NCBI
(17480)
Meta
(1609)
RP15
(1124)
RP35
(2507)
RP55
(3574)
RP75
(4626)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(99)
Full
(3260)
Representative proteomes UniProt
(12838)
NCBI
(17480)
Meta
(1609)
RP15
(1124)
RP35
(2507)
RP55
(3574)
RP75
(4626)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(99)
Full
(3260)
Representative proteomes UniProt
(12838)
NCBI
(17480)
Meta
(1609)
RP15
(1124)
RP35
(2507)
RP55
(3574)
RP75
(4626)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Pfam-B_760 (release 11.0)
Previous IDs: none
Type: Motif
Author: Finn RD
Number in seed: 99
Number in full: 3260
Average length of the domain: 63.30 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 10.44 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.5
Noise cut-off 21.3 21.3
Model length: 62
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 4 interactions for this family. More...

RMMBL Lactamase_B Lactamase_B Beta-Casp

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 RMMBL domain has been found. There are 52 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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