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17  structures 1331  species 1  interaction 2307  sequences 6  architectures

Family: GSP_synth (PF03738)

Summary: Glutathionylspermidine synthase preATP-grasp

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Glutathionylspermidine synthase preATP-grasp Provide feedback

This region contains the Glutathionylspermidine synthase enzymatic activity EC:6.3.1.8. This is the C-terminal region in bienzymes such as P43675. Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydrolysis of ATP (to ADP and Pi) with formation of an amide bond between spermidine and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly). In the pathogenic trypanosomatids, this reaction is the penultimate step in the biosynthesis of the antioxidant metabolite, trypanothione (N1,N8-bis-(glutathionyl)spermidine), and is a target for drug design [1]. This region, the pre-ATP grasp region, probably carries the substrate-binding site [2].

Literature references

  1. Bollinger JM Jr, Kwon DS, Huisman GW, Kolter R, Walsh CT; , J Biol Chem 1995;270:14031-14041.: Glutathionylspermidine metabolism in Escherichia coli. Purification, cloning, overproduction, and characterization of a bifunctional glutathionylspermidine synthetase/amidase. PUBMED:7775463 EPMC:7775463

  2. Pai CH, Chiang BY, Ko TP, Chou CC, Chong CM, Yen FJ, Chen S, Coward JK, Wang AH, Lin CH;, EMBO J. 2006;25:5970-5982.: Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase. PUBMED:17124497 EPMC:17124497


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005494

Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydrolysis of ATP (to ADP and Pi) with formation of an amide bond between spermidine and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly). In the pathogenic trypanosomatids, this reaction is the penultimate step in the biosynthesis of the antioxidant metabolite, trypanothione (N1,N8-bis-(glutathionyl)spermidine), and is a target for drug design [PUBMED:7775463]. This domain, the pre-ATP grasp domain, probably carries the substrate-binding site [PUBMED:17124497].

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 PreATP-grasp (CL0483), which has the following description:

This superfamily is characterised by bein g the copies of the domain that precedes the ATP-grasp domain common to all superfamily members, and it can contain a substrate-binding function.

The clan contains the following 2 members:

GSH_synthase GSP_synth

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
(159)
Full
(2307)
Representative proteomes NCBI
(1223)
Meta
(27)
RP15
(56)
RP35
(147)
RP55
(206)
RP75
(262)
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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
(159)
Full
(2307)
Representative proteomes NCBI
(1223)
Meta
(27)
RP15
(56)
RP35
(147)
RP55
(206)
RP75
(262)
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
(159)
Full
(2307)
Representative proteomes NCBI
(1223)
Meta
(27)
RP15
(56)
RP35
(147)
RP55
(206)
RP75
(262)
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: COG0754
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 159
Number in full: 2307
Average length of the domain: 99.70 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 22.57 %

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 22.4 22.4
Trusted cut-off 22.5 22.4
Noise cut-off 21.4 22.3
Model length: 97
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Interactions

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

CHAP

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 GSP_synth domain has been found. There are 17 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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