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18  structures 7662  species 0  interactions 7845  sequences 70  architectures

Family: FGAR-AT_linker (PF18072)

Summary: Formylglycinamide ribonucleotide amidotransferase linker domain

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Formylglycinamide ribonucleotide amidotransferase linker domain Provide feedback

This is the linker domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase ( EC:6.3.5.3), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway. The structure analysis of Salmonella typhimurium FGAR-AT reveals that this linker domain is made up of a long hydrophilic belt with an extended conformation [4].

Literature references

  1. Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA;, Proteins. 2006;63:1106-1111.: Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution. PUBMED:16544324 EPMC:16544324

  2. Morar M, Anand R, Hoskins AA, Stubbe J, Ealick SE;, Biochemistry. 2006;45:14880-14895.: Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily. PUBMED:17154526 EPMC:17154526

  3. Morar M, Hoskins AA, Stubbe J, Ealick SE;, Biochemistry. 2008;47:7816-7830.: Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation. PUBMED:18597481 EPMC:18597481

  4. Anand R, Hoskins AA, Stubbe J, Ealick SE;, Biochemistry. 2004;43:10328-10342.: Domain organization of Salmonella typhimurium formylglycinamide ribonucleotide amidotransferase revealed by X-ray crystallography. PUBMED:15301531 EPMC:15301531

  5. Tanwar AS, Morar M, Panjikar S, Anand R;, Acta Crystallogr D Biol Crystallogr. 2012;68:627-636.: Formylglycinamide ribonucleotide amidotransferase from Salmonella typhimurium: role of ATP complexation and the glutaminase domain in catalytic coupling. PUBMED:22683785 EPMC:22683785

  6. Tanwar AS, Goyal VD, Choudhary D, Panjikar S, Anand R;, PLoS One. 2013;8:e77781.: Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis. PUBMED:24223728 EPMC:24223728

  7. Suzuki S, Yanai H, Kanagawa M, Tamura S, Watanabe Y, Fuse K, Baba S, Sampei G, Kawai G;, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012;68:14-19.: Structure of N-formylglycinamide ribonucleotide amidotransferase II (PurL) from Thermus thermophilus HB8. PUBMED:22232163 EPMC:22232163


This tab holds annotation information from the InterPro database.

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Domain organisation

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Alignments

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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
(370)
Full
(7845)
Representative proteomes UniProt
(22204)
NCBI
(35616)
Meta
(1875)
RP15
(1973)
RP35
(5181)
RP55
(7842)
RP75
(11040)
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PP/heatmap 1                

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

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

Format an alignment

  Seed
(370)
Full
(7845)
Representative proteomes UniProt
(22204)
NCBI
(35616)
Meta
(1875)
RP15
(1973)
RP35
(5181)
RP55
(7842)
RP75
(11040)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(370)
Full
(7845)
Representative proteomes UniProt
(22204)
NCBI
(35616)
Meta
(1875)
RP15
(1973)
RP35
(5181)
RP55
(7842)
RP75
(11040)
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.

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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

This family is new in this Pfam release.

Seed source: ECOD:EUF01611
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 370
Number in full: 7845
Average length of the domain: 47.50 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 4.66 %

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 26.6 26.6
Trusted cut-off 26.7 26.6
Noise cut-off 26.5 26.5
Model length: 50
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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 FGAR-AT_linker domain has been found. There are 18 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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