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305  structures 7047  species 0  interactions 10533  sequences 56  architectures

Family: Ribonuc_red_sm (PF00268)

Summary: Ribonucleotide reductase, small chain

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This is the Wikipedia entry entitled "Ribonucleotide reductase". More...

Ribonucleotide reductase Edit Wikipedia article

Ribonucleotide reductase (RNR) uses radical-based chemistry to synthesize deoxyribonucleotides, the building blocks of DNA.

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.

Ribonucleotide reductase, small chain Provide feedback

No Pfam abstract.

Literature references

  1. Nordlund P, Eklund H; , J Mol Biol 1993;232:123-164.: Structure and function of the Escherichia coli ribonucleotide reductase protein R2. PUBMED:8331655 EPMC:8331655


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000358

Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase, ( EC ) [ PUBMED:3286319 , PUBMED:8511586 ] catalyses the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides: 2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H 2 O = ribonucleoside diphosphate + reduced thioredoxin

RNR provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, use a diiron-tyrosyl radical, Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria and bacteriophage, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes.

Class I ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain [ PUBMED:11875520 ]. The small chain binds two iron atoms [ PUBMED:2190093 ] (three Glu, one Asp, and two His are involved in metal binding) and contains an active site tyrosine radical. The regions of the sequence that contain the metal-binding residues and the active site tyrosine are conserved in ribonucleotide reductase small chain from prokaryotes, eukaryotes and viruses.

This family consist of the small subunit of class I ribonucleotide reductases. It also includes R2-like ligand-binding oxidase, which is homologous to the ribonucleotide reductase small subunit (R2), but whose function is still unknown [ PUBMED:19321420 , PUBMED:22976985 ].

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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Pfam Clan

This family is a member of clan Ferritin (CL0044), which has the following description:

The members of this clan all share a distinctive four helical bundle. The four helices are arranged antiparallel with a left-handed twist. This helical bundle is distinguished from others by the long connection between the second and third helices. Some of the members contain a Fe or Mn dimer at the centre of the helical bundle. The ferritin fold was first described by Murzin AG and Chothia C, Cur Opin Struc Biol 1992, 2:895-903.

The clan contains the following 27 members:

Ald_deCOase AOX AurF Coat_F COQ7 DUF2202 DUF2383 DUF305 DUF3231 DUF4142 DUF4439 DUF455 DUF5623 DUF6306 DUF6692 DUF892 FA_desaturase_2 Ferritin Ferritin-like Ferritin_2 MiaE MiaE_2 Mn_catalase PaaA_PaaC Phenol_Hydrox Ribonuc_red_sm Rubrerythrin

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
(268)
Full
(10533)
Representative proteomes UniProt
(40354)
RP15
(2176)
RP35
(5216)
RP55
(10064)
RP75
(16585)
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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
(268)
Full
(10533)
Representative proteomes UniProt
(40354)
RP15
(2176)
RP35
(5216)
RP55
(10064)
RP75
(16585)
Alignment:
Format:
Order:
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
(268)
Full
(10533)
Representative proteomes UniProt
(40354)
RP15
(2176)
RP35
(5216)
RP55
(10064)
RP75
(16585)
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: Prosite
Previous IDs: ribonuc_red; ribonuc_red_sm;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 268
Number in full: 10533
Average length of the domain: 265.9 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 76.79 %

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 33.6 33.6
Trusted cut-off 33.6 33.6
Noise cut-off 33.5 33.5
Model length: 280
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Ribonuc_red_sm domain has been found. There are 305 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044SJZ6 View 3D Structure Click here
A0A077YX22 View 3D Structure Click here
A0A077ZQJ3 View 3D Structure Click here
A0A0D2H5A5 View 3D Structure Click here
A0A0H3GU80 View 3D Structure Click here
A0A0H3GVM6 View 3D Structure Click here
A0A0H3GYJ3 View 3D Structure Click here
A0A0H5S7V6 View 3D Structure Click here
A0A0K0DV53 View 3D Structure Click here
A0A0N4UEA7 View 3D Structure Click here
A0A0R4J5J3 View 3D Structure Click here
A0A0R4J618 View 3D Structure Click here
A0A1C1C935 View 3D Structure Click here
A0A1D8PI17 View 3D Structure Click here
A0QPD3 View 3D Structure Click here
A1TAR1 View 3D Structure Click here
A1UKW4 View 3D Structure Click here
A4F7B2 View 3D Structure Click here
A4I2X5 View 3D Structure Click here
B4FAZ9 View 3D Structure Click here
B4FEF8 View 3D Structure Click here
C0NFK8 View 3D Structure Click here
C1GV26 View 3D Structure Click here
C4QCA2 View 3D Structure Click here
D4A7M6 View 3D Structure Click here
D4ADQ1 View 3D Structure Click here
E9AGZ9 View 3D Structure Click here
I1JQ20 View 3D Structure Click here
J9EMH6 View 3D Structure Click here
K0FAD3 View 3D Structure Click here
K7W7U8 View 3D Structure Click here
O30601 View 3D Structure Click here
O67475 View 3D Structure Click here
O83092 View 3D Structure Click here
O84835 View 3D Structure Click here
P09938 View 3D Structure Click here
P0DKH2 View 3D Structure Click here
P11157 View 3D Structure Click here
P17424 View 3D Structure Click here
P31350 View 3D Structure Click here