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12  structures 321  species 0  interactions 620  sequences 29  architectures

Family: PRORP (PF16953)

Summary: Protein-only RNase P

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Protein-only RNase P Provide feedback

PRORPs (protein-only RNase P) are a class of RNA processing enzymes that catalyze maturation of the 5′ end of precursor tRNAs in Eukaryotes [1]. Arabidopsis thaliana contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) where PRORP1 localizes to mitochondria as well as chloroplasts, while PRORP2 and PRORP3 are found in the nucleus. In humans and most other metazoans, mt-RNase P is composed of three protein subunits (mitochondrial RNase P proteins 1–3; MRPP1-3), homologs to the Arabidopsis thaliana PRORP1-3. This domain corresponds to the metallonuclease domain of PRORPs. PRORP1 has 22% sequence identity to the human homologue MRPP3. PRORP1 crystal structure shows a V-shaped tripartite structure with a C-terminal metallonuclease domain of the NYN (N4BL1, YacP-like nuclease) family, with a typical and functional two-metal-ion catalytic site that has conserved aspartate residues [2].

Literature references

  1. Karasik A, Shanmuganathan A, Howard MJ, Fierke CA, Koutmos M;, J Mol Biol. 2016;428:26-40.: Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5' End Processing Enzymes. PUBMED:26655022 EPMC:26655022

  2. Reinhard L, Sridhara S, Hallberg BM;, Nucleic Acids Res. 2015;43:5664-5672.: Structure of the nuclease subunit of human mitochondrial RNase P. PUBMED:25953853 EPMC:25953853


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR031595

This entry represents a domain found in protein-only RNase P (PRORP), an enzyme that processes precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. PRORP catalyses the maturation of the 5' ends of tRNA precursors [PUBMED:22991464].

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 PIN (CL0280), which has the following description:

This superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.

The clan contains the following 18 members:

5_3_exonuc_N DUF188 DUF4411 Fcf1 Mut7-C NYN NYN_YacP PIN PIN_2 PIN_3 PIN_4 PIN_5 PIN_6 PRORP RNase_Zc3h12a RNase_Zc3h12a_2 XPG_N XRN_N

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...

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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
(18)
Full
(620)
Representative proteomes UniProt
(869)
NCBI
(1372)
Meta
(3)
RP15
(131)
RP35
(290)
RP55
(469)
RP75
(556)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(18)
Full
(620)
Representative proteomes UniProt
(869)
NCBI
(1372)
Meta
(3)
RP15
(131)
RP35
(290)
RP55
(469)
RP75
(556)
Alignment:
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  Seed
(18)
Full
(620)
Representative proteomes UniProt
(869)
NCBI
(1372)
Meta
(3)
RP15
(131)
RP35
(290)
RP55
(469)
RP75
(556)
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.

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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: PDB:4g23
Previous IDs: none
Type: Domain
Author: Eberhardt RY, El-Gebali S
Number in seed: 18
Number in full: 620
Average length of the domain: 199.60 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 37.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 241
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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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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 PRORP domain has been found. There are 12 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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