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70  structures 6173  species 2  interactions 7362  sequences 55  architectures

Summary: Dihydroneopterin aldolase

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

Dihydroneopterin aldolase

dihydroneopterin aldolase
oktamer
Identifiers
EC number4.1.2.25
CAS number37290-59-8
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structures
Gene Ontology
Dihydroneopterin aldolase
crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine
Identifiers
SymbolFolB
PfamPF02152
Pfam clanCL0334
InterProIPR006157
SCOPe1b9l / SUPFAM

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 ${\displaystyle \rightleftharpoons }$ 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): 3015â€“25. PMID 4912541.

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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.

Dihydroneopterin aldolase

This enzyme EC:4.1.2.25 catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate.

Literature references

1. Haussmann C, Rohdich F, Schmidt E, Bacher A, Richter G; , J Biol Chem 1998;273:17418-17424.: Biosynthesis of pteridines in Escherichia coli. Structural and mechanistic similarity of dihydroneopterin-triphosphate epimerase and dihydroneopterin aldolase. PUBMED:9651328 EPMC:9651328

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006157

Dihydroneopterin aldolase (DHNA or folB) catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate [PUBMED:12039964]. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids, as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate and DHNA is one enzyme in this pathway. In the opportunistic pathogen Pneumocystis carinii, dihydroneopterin aldolase function is expressed as the N-terminal portion of the multifunctional folic acid synthesis protein (Fas). This region encompasses two domains, FasA and FasB, which are 27% amino acid identical [PUBMED:9709001]. FasA and FasB also share significant amino acid sequence similarity with bacterial dihydroneopterin aldolases.

This entry also includes 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE or folX). Though it is known that DHNTPE catalyzes the epimerization of dihydroneopterin triphosphate to dihydromonapterin triphosphate, the biological role of this enzyme is still unclear. It is hypothesized that it is not an essential protein since a folX knockout in E. coli has a normal phenotype and the fact that folX is not present in H. influenza [PUBMED:9182560,PUBMED:9006053]. DHNA and DHNTPE have been shown to be able to compensate for the other's activity albeit at slower reaction rates [PUBMED:9651328]. The functional enzyme for both is an octamer of identical subunits. Mammals lack many of the enzymes in the folate pathway including, DHNA and DHNTPE.

This region consists of two tandem sequences each homologous to folB and which form tetramers [PUBMED:10737935].

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 THBO-biosyn (CL0334), which has the following description:

The families in this clan bind purine or ptein in topologically similar sites between subunits.

The clan contains the following 7 members:

FolB

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
(849)
Full
(7362)
Representative proteomes UniProt
(31269)
NCBI
(34523)
Meta
(2077)
RP15
(886)
RP35
(3365)
RP55
(7124)
RP75
(12520)
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PP/heatmap 1

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

Key: available, not generated, not available.

Format an alignment

Seed
(849)
Full
(7362)
Representative proteomes UniProt
(31269)
NCBI
(34523)
Meta
(2077)
RP15
(886)
RP35
(3365)
RP55
(7124)
RP75
(12520)
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
(849)
Full
(7362)
Representative proteomes UniProt
(31269)
NCBI
(34523)
Meta
(2077)
RP15
(886)
RP35
(3365)
RP55
(7124)
RP75
(12520)
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

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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

 Seed source: PSI-BLAST P31055 Previous IDs: none Type: Domain Sequence Ontology: SO:0000417 Author: Bateman A Number in seed: 849 Number in full: 7362 Average length of the domain: 110.60 aa Average identity of full alignment: 27 % Average coverage of the sequence by the domain: 61.26 %

HMM information

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 31.8 31.8
Trusted cut-off 32.3 32.2
Noise cut-off 31.5 31.7
Model length: 111
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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 Archea Eukaryota Bacteria Other sequences Viruses Unclassified Viroids Unclassified sequence

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Interactions

There are 2 interactions for this family. More...

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 FolB domain has been found. There are 70 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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