Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
7  structures 1748  species 1  interaction 1866  sequences 6  architectures

Family: GCHY-1 (PF02649)

Summary: Type I GTP cyclohydrolase folE2

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Type I GTP cyclohydrolase folE2 Provide feedback

This is a family of prokaryotic proteins with type I GTP cyclohydrolase activity. GTP cyclohydrolase I is the first enzyme of the de novo tetrahydrofolate biosynthetic pathway present in bacteria, fungi, and plants, and encoded in Escherichia coli by the folE gene; it is also the first enzyme of the biopterin (BH4) pathway in Homo [1]. The invariate, highly conserved glutamate residue at position 216 in Q5F9K6 is likely to be the substrate ligand and the metal ligand is likely to be the cysteine at position 147. The enzyme is Zinc 2+ dependent [2].

Literature references

  1. El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crecy-Lagard V;, J Biol Chem. 2006;281:37586-37593.: Discovery of a new prokaryotic type I GTP cyclohydrolase family. PUBMED:17032654 EPMC:17032654

  2. Sankaran B, Bonnett SA, Shah K, Gabriel S, Reddy R, Schimmel P, Rodionov DA, de Crecy-Lagard V, Helmann JD, Iwata-Reuyl D, Swairjo MA;, J Bacteriol. 2009;191:6936-6949.: Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. PUBMED:19767425 EPMC:19767425


This tab holds annotation information from the InterPro database.

InterPro entry IPR003801

This is a family of prokaryotic/archaeal proteins with type I GTP cyclohydrolase activity. GTP cyclohydrolase I is the first enzyme of the de novo tetrahydrofolate biosynthetic pathway present in bacteria, fungi, and plants, and encoded in Escherichia coli by the folE gene [PUBMED:17032654]. FolE is Zinc 2+ dependent [PUBMED:19767425].

In bacteria GTP cyclohydrolase FolE2 converts GTP to 7,8-dihydroneopterin triphosphate [PUBMED:17032654]; while in the archaea GTP cyclohydrolase MptA converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate, the first intermediate in the biosynthesis of coenzyme methanopterin [PUBMED:17497938].

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...

Loading domain graphics...

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 GCHY-1 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 (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...

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
(235)
Full
(1866)
Representative proteomes UniProt
(5527)
NCBI
(7105)
Meta
(284)
RP15
(466)
RP35
(1266)
RP55
(1866)
RP75
(2623)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(235)
Full
(1866)
Representative proteomes UniProt
(5527)
NCBI
(7105)
Meta
(284)
RP15
(466)
RP35
(1266)
RP55
(1866)
RP75
(2623)
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
(235)
Full
(1866)
Representative proteomes UniProt
(5527)
NCBI
(7105)
Meta
(284)
RP15
(466)
RP35
(1266)
RP55
(1866)
RP75
(2623)
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

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: COG1469
Previous IDs: DUF198;
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 235
Number in full: 1866
Average length of the domain: 262.10 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 88.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 28.2 33.2
Noise cut-off 24.3 23.6
Model length: 259
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

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

GCHY-1

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 GCHY-1 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.

Loading structure mapping...