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7  structures 1203  species 0  interactions 1443  sequences 3  architectures

Family: YfbR-like (PF12917)

Summary: 5'-deoxynucleotidase YfbR-like

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5'-deoxynucleotidase YfbR-like Provide feedback

This entry contains Escherichia coli (strain K12) YfbR. It a 5'-deoxynucleotidase that functions as a dCMP phosphohydrolase in a salvage pathway for the synthesis of dUMP in a dcd/deoA mutant [1]. YfbR contains a conserved HD domain [2]. YfbR has phosphatase activity with deoxyribonucleoside 5'-monophosphates and does not hydrolyze ribonucleotides or deoxyribonucloside 3'-monophosphates [2,3]. Crystal structures of YfbR have been solved, it was suggested that the biological unit is a dimer [4]. This family also includes phage HD domain-containing hydrolase-like enzymes, such as A0A2H5BHG9 and A0A2L0V156 from Acinetobacter phage SH-Ab15497 [5] which are associated with PurZ, an enzyme that catalyses the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity. They have 2'-deoxyadenine 5'-triphosphate triphosphohydrolase (dATPase) activity and catalyse the hydrolysis of 2'-deoxyadenine 5'-triphosphate dATP to 2'-deoxyadenine (dA) and triphosphate. These enzymes are highly specific for dATP and also catalyse the hydrolysis of dADP and dAMP into dA, releasing pyrophosphate and phosphate, respectively. Thus, these dATPases facilitate the synthesis of Z-genome synthesis removing dATP and dADP from the nucleotide pool of the host [5].

Literature references

  1. Weiss B;, J Bacteriol. 2007;189:7922-7926.: The deoxycytidine pathway for thymidylate synthesis in Escherichia coli. PUBMED:17827303 EPMC:17827303

  2. Proudfoot M, Kuznetsova E, Brown G, Rao NN, Kitagawa M, Mori H, Savchenko A, Yakunin AF;, J Biol Chem. 2004;279:54687-54694.: General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG. PUBMED:15489502 EPMC:15489502

  3. Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF;, FEMS Microbiol Rev. 2005;29:263-279.: Enzyme genomics: Application of general enzymatic screens to discover new enzymes. PUBMED:15808744 EPMC:15808744

  4. Zimmerman MD, Proudfoot M, Yakunin A, Minor W;, J Mol Biol. 2008;378:215-226.: Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli. PUBMED:18353368 EPMC:18353368

  5. Zhou Y, Xu X, Wei Y, Cheng Y, Guo Y, Khudyakov I, Liu F, He P, Song Z, Li Z, Gao Y, Ang EL, Zhao H, Zhang Y, Zhao S;, Science. 2021;372:512-516.: A widespread pathway for substitution of adenine by diaminopurine in phage genomes. PUBMED:33926954 EPMC:33926954


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022971

This entry contains Escherichia coli (strain K12) YfbR. It is a 5'-deoxynucleotidase that functions as a dCMP phosphohydrolase in a salvage pathway for the synthesis of dUMP in a dcd/deoA mutant [ PUBMED:17827303 ]. YfbR contains a conserved HD domain [ PUBMED:15489502 ]. YfbR has phosphatase activity with deoxyribonucleoside 5'-monophosphates and does not hydrolyze ribonucleotides or deoxyribonucloside 3'-monophosphates [ PUBMED:15489502 ]. Nucleotidase activity of YfbR was discovered in a high-throughput screen of purified proteins [ PUBMED:15808744 ]. Crystal structures of YfbR have been solved; based on an analysis of crystal packing and size-exclusion chromatography, it was suggested that the biological unit is a dimer. Site-directed mutagenesis confirmed the importance of certain conserved active site residues, and mechanisms for substrate selectivity and catalysis were proposed [ PUBMED:18353368 ].

This family also includes phage HD domain-containing hydrolase-like enzymes, such as A0A2H5BHG9 and A0A2L0V156 from Acinetobacter phage SH-Ab 15497 [ PUBMED:33926954 ], which are associated with PurZ, an enzyme that catalyses the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity. They have 2'-deoxyadenine 5'-triphosphate triphosphohydrolase (dATPase) activity, and catalyse the hydrolysis of 2'-deoxyadenine 5'-triphosphate (dATP) to 2'-deoxyadenine (dA) and triphosphate, with the highest activity using Co2+ as the divalent metal cofactor. These enzymes are highly specific for dATP and also catalyse the hydrolysis of dADP and dAMP into dA, releasing pyrophosphate and phosphate, respectively. Thus, these dATPases facilitate the synthesis of Z-genome synthesis removing dATP and dADP from the nucleotide pool of the host [ PUBMED:33926954 ].

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 HD_PDEase (CL0237), which has the following description:

This clan includes a range of phosphohydrolase enzymes with a common helical fold.

The clan contains the following 13 members:

DUF4202 HD HD_3 HD_4 HD_5 HD_6 HDOD MIOX PDEase_I SidE_PDE TraI_2 tRNA_NucTran2_2 YfbR-like

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
(83)
Full
(1443)
Representative proteomes UniProt
(7381)
RP15
(204)
RP35
(738)
RP55
(1484)
RP75
(2702)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(83)
Full
(1443)
Representative proteomes UniProt
(7381)
RP15
(204)
RP35
(738)
RP55
(1484)
RP75
(2702)
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
(83)
Full
(1443)
Representative proteomes UniProt
(7381)
RP15
(204)
RP35
(738)
RP55
(1484)
RP75
(2702)
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: JCSG_target_394139
Previous IDs: HD_1; HD_2;
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 83
Number in full: 1443
Average length of the domain: 166.80 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 82.77 %

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 25.9 25.9
Trusted cut-off 25.9 25.9
Noise cut-off 25.8 25.8
Model length: 182
Family (HMM) version: 10
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 YfbR-like domain has been found. There are 7 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
Q2G277 View 3D Structure Click here