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60  structures 3833  species 1  interaction 4525  sequences 22  architectures

Family: FolB (PF02152)

Summary: Dihydroneopterin aldolase

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

Dihydroneopterin aldolase Edit Wikipedia article

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
PDB 1sql EBI.jpg
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.

[edit] 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.

[edit] 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 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.

Dihydroneopterin aldolase Provide feedback

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 catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. 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. FasA and FasB also share significant amino acid sequence similarity with bacterial dihydroneopterin aldolases.

This region consists of two tandem sequences each homologous to folB and which form tetramers [PUBMED:9709001].

Gene Ontology

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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 contains the following 6 members:

FolB GTP_cyclohydroI PTPS QueF QueF_N Uricase

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.

  Seed
(129)
Full
(4525)
Representative proteomes NCBI
(2777)
Meta
(2126)
RP15
(309)
RP35
(627)
RP55
(864)
RP75
(1029)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(129)
Full
(4525)
Representative proteomes NCBI
(2777)
Meta
(2126)
RP15
(309)
RP35
(627)
RP55
(864)
RP75
(1029)
Alignment:
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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
(129)
Full
(4525)
Representative proteomes NCBI
(2777)
Meta
(2126)
RP15
(309)
RP35
(627)
RP55
(864)
RP75
(1029)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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.

Pfam alignments:

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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 View help on the curation process

Seed source: PSI-BLAST P31055
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 129
Number in full: 4525
Average length of the domain: 111.20 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 72.22 %

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 24.1 24.1
Trusted cut-off 24.1 24.4
Noise cut-off 23.6 23.3
Model length: 113
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

FolB

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 60 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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