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1  structure 5  species 0  interactions 5  sequences 3  architectures

Family: Stirrup (PF09061)

Summary: Stirrup

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This is the Wikipedia entry entitled "Stirrup protein domain". More...

Stirrup protein domain Edit Wikipedia article

Stirrup
PDB 1dq3 EBI.jpg
crystal structure of an archaeal intein-encoded homing endonuclease pi-pfui
Identifiers
Symbol Stirrup
Pfam PF09061
InterPro IPR015146
SCOP 1dq3
SUPERFAMILY 1dq3

In molecular biology, the protein domain Stirrup is a domain, found only in found in the domain, archaea. The Stirrup protein domain is found in prokaryotic protein ribonucleotide reductases. It obtains its name due to its resemblance to an old fashioned Japanese stirrup. Stirrip has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges distributed on its surface.[1]

Function[edit]

This protein domain provides the precursors necessary for DNA synthesis. It catalyses the biosynthesis of DNA from RNA.[2]

Structure[edit]

This structure contains a three-stranded beta-sheet to the solvent, which lies against alpha-helices.[1]

References[edit]

  1. ^ a b Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K (July 2000). "Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI". J. Mol. Biol. 300 (4): 889–901. doi:10.1006/jmbi.2000.3873. PMID 10891276. 
  2. ^ "Ribonucleoside-diphosphate reductase". UniProt. Retrieved 14 August 2012. 

This article incorporates text from the public domain Pfam and InterPro IPR015146

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.

Stirrup Provide feedback

The Stirrup domain, found in the prokaryotic protein ribonucleotide reductase, has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges distributed on its surface [1].

Literature references

  1. Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K; , J Mol Biol. 2000;300:889-901.: Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI. PUBMED:10891276 EPMC:10891276


External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

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(3)
Full
(5)
Representative proteomes NCBI
(5)
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(1)
RP35
(1)
RP55
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(3)
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  Seed
(3)
Full
(5)
Representative proteomes NCBI
(5)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(2)
RP75
(3)
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
(3)
Full
(5)
Representative proteomes NCBI
(5)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(2)
RP75
(3)
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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.

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

This family is new in this Pfam release.

Seed source: pdb_1dq3
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 3
Number in full: 5
Average length of the domain: 79.00 aa
Average identity of full alignment: 80 %
Average coverage of the sequence by the domain: 4.54 %

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 25.2 150.5
Noise cut-off 24.6 23.4
Model length: 79
Family (HMM) version: 1
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 Stirrup domain has been found. There are 1 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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