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14  structures 82  species 2  interactions 84  sequences 1  architecture

# Summary: Domain of unknown function (DUF372)

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

This is the Wikipedia entry entitled "Dihydroneopterin aldolase". More...

# Dihydroneopterin aldolase

dihydroneopterin aldolase
Identifiers
EC number 4.1.2.25
CAS number 37290-59-8
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Dihydroneopterin aldolase
crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine
Identifiers
Symbol FolB
Pfam PF02152
Pfam clan CL0334
InterPro IPR006157
SCOP 1b9l
SUPERFAMILY 1b9l

In enzymology, a dihydroneopterin aldolase (EC 4.1.2.25) is an enzyme that catalyzes the chemical reaction

2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8- dihydropteridine $\rightleftharpoons$ 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + glycolaldehyde

Thus, the substrate (biochemistry) of this enzyme is 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine, whereas its two products are 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine and glycolaldehyde.

This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropt eridine glycolaldehyde-lyase (2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine-forming). Other names in common use include 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-, and dihydropteridine glycolaldehyde-lyase. This enzyme participates in folate biosynthesis.

## Structural studies

As of late 2007, 13 structures have been solved for this class of enzymes, with PDB accession codes 1NBU, 1RRI, 1RRW, 1RRY, 1RS2, 1RS4, 1RSD, 1RSI, 1U68, 1Z9W, 2CG8, 2NM2, and 2NM3.

## References

• Mathis JB, Brown GM (1970). "The biosynthesis of folic acid. XI. Purification and properties of dihydroneopterin aldolase". J. Biol. Chem. 245 (11): 3015–25. PMID 4912541.

This is the Wikipedia entry entitled "Domain of unknown function". More...

# Domain of unknown function

A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.[1]

## History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[2] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

## Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[3] This work showed that about two thirds of DUF families had a structure similar to a previously solved one and therefore likely to be divergent members of existing protein superfamilies, whereas about one third possessed a novel protein fold.

## Frequency and conservation

Protein domains and DUFs in different domains of life. Left: Annotated domains. Right: domains of unknown function. Not all overlaps shown.[4]

More than 20% of all protein domains were annotated as DUFs in 2013. About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs.[4]

Many DUFs are highly conserved, indicating an important role in biology. However, many such DUFs are not essential, hence their biological role often remains unknown. For instance, DUF143 is present in most bacteria and eukaryotic genomes.[5] However, when it was deleted in Escherichia coli no obvious phenotype was obvious. Later it was shown that the proteins that contain DUF143, are ribosomal silencing factors that block the assembly of the two ribosomal subunits.[5] While this function is not essential, it helps the cells to adapt to low nutrient conditions by shutting down protein biosynthesis. As a result, these proteins and the DUF only becomes relevant when the cells starve.[5]

## Essential DUFs (eDUFs)

Goodacre et al. identified 238 DUFs in 355 essential proteins (in 16 model bacterial species), most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. These DUFs are called "essential DUFs" or eDUFs.[4]

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.

# Domain of unknown function (DUF372)

Domain of unknown function.

This tab holds annotation information from the InterPro database.

# InterPro entry IPR007179

This is a group of proteins of unknown function. It is found N-terminal to another domain of unknown function (INTERPRO).

# Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

# 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...

## 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
(15)
Full
(84)
Representative proteomes NCBI
(90)
Meta
(6)
RP15
(11)
RP35
(41)
RP55
(52)
RP75
(60)
Jalview View  View  View  View  View  View  View  View
HTML View  View  View  View  View  View
PP/heatmap 1 View  View  View  View  View
Pfam viewer View  View

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

Key: available, not generated, not available.

## Format an alignment

Seed
(15)
Full
(84)
Representative proteomes NCBI
(90)
Meta
(6)
RP15
(11)
RP35
(41)
RP55
(52)
RP75
(60)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(15)
Full
(84)
Representative proteomes NCBI
(90)
Meta
(6)
RP15
(11)
RP35
(41)
RP55
(52)
RP75
(60)

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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.

 Pfam alignments: Seed (15) Full (84)

# 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.

# 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

 Seed source: COG2098 Previous IDs: none Type: Family Author: Kerrison ND, Finn RD Number in seed: 15 Number in full: 84 Average length of the domain: 38.00 aa Average identity of full alignment: 56 % Average coverage of the sequence by the domain: 31.52 %

## HMM information

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 20.4 20.4
Trusted cut-off 21.0 40.5
Noise cut-off 19.9 20.3
Model length: 38
Family (HMM) version: 7

# Species distribution

### Sunburst controls

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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...

### Tree controls

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The tree shows the occurrence of this domain across different species. More...