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134  structures 4552  species 3  interactions 8265  sequences 42  architectures

Family: Pterin_bind (PF00809)

Summary: Pterin binding enzyme

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 "Dihydropteroate synthase". More...

Dihydropteroate synthase Edit Wikipedia article

Dihydropteroate synthase
THFsynthesispathway.png
Tetrahydrofolate synthesis pathway
Identifiers
EC number 2.5.1.15
CAS number 9055-61-2
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
Pterin binding enzyme
Identifiers
Symbol Pterin_bind
Pfam PF00809
InterPro IPR000489
PROSITE PDOC00630
SCOP 1ajz
SUPERFAMILY 1ajz

Dihydropteroate synthase is an enzyme classified under EC 2.5.1.15. It produces dihydropteroate in bacteria, but it is not expressed in most eukaryotes including humans. This makes it a useful target for sulfonamide antibiotics, which compete with the PABA precursor.

All organisms require reduced folate cofactors for the synthesis of a variety of metabolites. Most microorganisms must synthesize folate de novo because they lack the active transport system of higher vertebrate cells that allows these organisms to use dietary folates. Proteins containing this domain include dihydropteroate synthase (EC 2.5.1.15) as well as a group of methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulphur protein methyltransferase (MeTr) Q46389 that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation.

Dihydropteroate synthase (EC 2.5.1.15) (DHPS) catalyses the condensation of 6-hydroxymethyl-7,8-dihydropteridine pyrophosphate to para-aminobenzoic acid to form 7,8-dihydropteroate. This is the second step in the three-step pathway leading from 6-hydroxymethyl-7,8-dihydropterin to 7,8-dihydrofolate. DHPS is the target of sulphonamides, which are substrate analogues that compete with para-aminobenzoic acid. Bacterial DHPS (gene sul or folP)[1] is a protein of about 275 to 315 amino acid residues that is either chromosomally encoded or found on various antibiotic resistance plasmids. In the lower eukaryote Pneumocystis carinii, DHPS is the C-terminal domain of a multifunctional folate synthesis enzyme (gene fas).[2]

References[edit]

  1. ^ Crawford IP, Slock J, Stahly DP, Six EW, Han CY (1990). "An apparent Bacillus subtilis folic acid biosynthetic operon containing pab, an amphibolic trpG gene, a third gene required for synthesis of para-aminobenzoic acid, and the dihydropteroate synthase gene". J. Bacteriol. 172 (12): 7211–7226. PMC 210846. PMID 2123867. 
  2. ^ Volpe F, Dyer M, Scaife JG, Darby G, Stammers DK, Delves CJ (1992). "The multifunctional folic acid synthesis fas gene of Pneumocystis carinii appears to encode dihydropteroate synthase and hydroxymethyldihydropterin pyrophosphokinase". Gene 112 (2): 213–218. doi:10.1016/0378-1119(92)90378-3. PMID 1313386. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR000489


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.

Pterin binding enzyme Provide feedback

This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase EC:2.5.1.15 as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) Q46389 that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide centre in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin [2].

Literature references

  1. Achari A, Somers DO, Champness JN, Bryant PK, Rosemond J, Stammers DK , Nat Struct Biol 1997;4:490-497.: Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase. PUBMED:9187658 EPMC:9187658

  2. Doukov T, Seravalli J, Stezowski JJ, Ragsdale SW; , Structure Fold Des 2000;8:817-830.: Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. PUBMED:10997901 EPMC:10997901


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000489

The ~250-residue pterin-binding domain has been shown to adopt a (beta/alpha)8 barrel fold, which has the overall shape of a distorted cylinder. It has eight alpha-helices stacked around the outside of an inner cylinder of parallel beta-strands. The pterin ring binds at the bottom of the (beta/alpha;)8 barrel in a polar cup-like region that is relatively solvent exposed and fairly negatively charged. The pterin ring is partially buried within the (beta/alpha)8 barrel. The pterin binding residues are highly conserved and include aspartate and asparagine residues located at the C terminus of the beta-strands of the barrel, which are predicted to form hydrogen bonds with the nitrogen and oxygen atoms of the pterin ring [PUBMED:10997901, PUBMED:9187658, PUBMED:14752199].

Some proteins known to contain a pterin-binding domain are listed below:

  • Prokaryotic and eukaryotic B12-dependent methionine synthase (MetH) (EC), a large, modular protein that catalyzes the transfer of a methyl group from methyltetrahydrofolate (CH3-H4folate) to Hcy to form methionine, using cobalamin as an intermediate methyl carrier.
  • Prokaryotic and eukaryotic dihydropteroate synthase (DHPS) (EC). It catalyzes the condensation of para-aminobenzoic acid (pABA) with 7,8- dihydropterin-pyrophosphate (DHPPP), eliminating pyrophosphate to form 7,8- dihydropteroate which is subsequently converted to tetrahydrofolate.
  • Moorella thermoacetica 5-methyltetrahydrofolate corrinoid/iron sulphur protein methyltransferase (MeTr). It transfers the N5-methyl group from CH3-H4folate to a cob(I)amide centre in another protein, the corrinoid iron sulphur protein.

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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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
(42)
Full
(8265)
Representative proteomes NCBI
(6541)
Meta
(3687)
RP15
(718)
RP35
(1410)
RP55
(1818)
RP75
(2104)
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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
(42)
Full
(8265)
Representative proteomes NCBI
(6541)
Meta
(3687)
RP15
(718)
RP35
(1410)
RP55
(1818)
RP75
(2104)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(42)
Full
(8265)
Representative proteomes NCBI
(6541)
Meta
(3687)
RP15
(718)
RP35
(1410)
RP55
(1818)
RP75
(2104)
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.

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: Pfam-B_1411 (release 2.1) and Pfam-B_3423 (release 6.6)
Previous IDs: DHPS;
Type: Domain
Author: Bateman A
Number in seed: 42
Number in full: 8265
Average length of the domain: 202.90 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 37.28 %

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 25.5 25.5
Trusted cut-off 25.7 25.5
Noise cut-off 25.4 25.4
Model length: 210
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Pterin_bind HPPK S-methyl_trans

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 Pterin_bind domain has been found. There are 134 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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