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19  structures 4503  species 3  interactions 4769  sequences 45  architectures

Family: GARS_A (PF01071)

Summary: Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain

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 "Phosphoribosylamine-glycine ligase". More...

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.

Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain Provide feedback

Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase (see PF02786).

Literature references

  1. Aiba A, Mizobuchi K; , J Biol Chem 1989;264:21239-21246.: Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli. PUBMED:2687276 EPMC:2687276

  2. Wang W, Kappock TJ, Stubbe J, Ealick SE; , Biochemistry 1998;37:15647-15662.: X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. PUBMED:9843369 EPMC:9843369


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020561

Phosphoribosylglycinamide synthetase (EC) (GARS) (phosphoribosylamine glycine ligase) [PUBMED:2687276] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (INTERPRO), forming GARS-AIRS-GART.

This entry represents the A-domain of the enzyme, and is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase.

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 ATP-grasp (CL0179), which has the following description:

The ATP-grasp domain is found in a wide variety of carboxylate-amine/thiol ligases [1]. It is composed of two subdomains, with ATP being bound in the cleft between the two.

The clan contains the following 20 members:

ATP-grasp ATP-grasp_2 ATP-grasp_3 ATP-grasp_4 ATP-grasp_5 ATPgrasp_ST ATPgrasp_Ter ATPgrasp_TupA ATPgrasp_YheCD CP_ATPgrasp_1 CP_ATPgrasp_2 CPSase_L_D2 Dala_Dala_lig_C DUF1297 GARS_A GSH-S_ATP Ins134_P3_kin RimK Synapsin_C TTL

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...

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
(19)
Full
(4769)
Representative proteomes NCBI
(7505)
Meta
(5005)
RP15
(403)
RP35
(790)
RP55
(1057)
RP75
(1247)
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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
(19)
Full
(4769)
Representative proteomes NCBI
(7505)
Meta
(5005)
RP15
(403)
RP35
(790)
RP55
(1057)
RP75
(1247)
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
(19)
Full
(4769)
Representative proteomes NCBI
(7505)
Meta
(5005)
RP15
(403)
RP35
(790)
RP55
(1057)
RP75
(1247)
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_916 (release 3.0)
Previous IDs: GARS;
Type: Domain
Author: Finn RD, Bateman A, Griffiths-Jones SR
Number in seed: 19
Number in full: 4769
Average length of the domain: 188.90 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 41.23 %

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 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 194
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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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...

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Interactions

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

GARS_A GARS_C GARS_N

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 GARS_A domain has been found. There are 19 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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