2IO8 | pdb_00002io8

E. coli Bifunctional glutathionylspermidine synthetase/amidase Incomplex with Mg2+ and ADP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2io8b1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Glutathionylspermidine synthase substrate-binding domain-like	Glutathionylspermidine synthase, synthetase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2io8b2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	CHAP domain	Glutathionylspermidine synthase, amidase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2io8b3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Glutathionylspermidine synthase ATP-binding domain-like	Glutathionylspermidine synthase, synthetase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2io8a1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Glutathionylspermidine synthase substrate-binding domain-like	Glutathionylspermidine synthase, synthetase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2io8a2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	CHAP domain	Glutathionylspermidine synthase, amidase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2io8a3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Glutathionylspermidine synthase ATP-binding domain-like	Glutathionylspermidine synthase, synthetase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PreATP-grasp domain	8042817	3001680	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8042818	3000094	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8042818	3000094	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8042819	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PreATP-grasp domain	8042817	3001680	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8042819	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8042818	3000094	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8042818	3000094	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	LRR_6,LRR_RI_capping	e2io8B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.1)
B	Phage_lysozyme	e2io8B2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Phage_lysozyme	ECOD (v294.1)
B	GBP	e2io8B3	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: GBP	ECOD (v294.1)
A	GSP_synth	e2io8A1	A: beta duplicates or obligate multimers	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: GSP_synth	ECOD (v294.1)
A	CHAP	e2io8A2	A: few secondary structure elements	X: Cysteine proteinases-like	H: Cysteine proteinases	T: Cysteine proteinases	F: CHAP	ECOD (v294.1)
A		e2io8A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.1720.10	Alpha Beta	Alpha-Beta Complex	endopeptidase fold (from Nostoc punctiforme)	endopeptidase domain like (from Nostoc punctiforme)	CATH (4.3.0)
A	3.90.1720.10	Alpha Beta	Alpha-Beta Complex	endopeptidase fold (from Nostoc punctiforme)	endopeptidase domain like (from Nostoc punctiforme)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03738	Glutathionylspermidine synthase preATP-grasp (GSP_synth)	Glutathionylspermidine synthase preATP-grasp	This region contains the Glutathionylspermidine synthase enzymatic activity EC:6.3.1.8. This is the C-terminal region in bi-enzymes such as Swiss:P43675. Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydroly ...	This region contains the Glutathionylspermidine synthase enzymatic activity EC:6.3.1.8. This is the C-terminal region in bi-enzymes such as Swiss: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].	Domain
A, B	PF05257	CHAP domain (CHAP)	CHAP domain	This domain corresponds to an amidase function. Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of Swiss:P43675, where it functions as a glutathionylspermidine amidase EC:3.5.1.78 [1]. ...	This domain corresponds to an amidase function. Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of Swiss:P43675, where it functions as a glutathionylspermidine amidase EC:3.5.1.78 [1]. This domain is found to be the catalytic domain of PlyCA [4]. CHAP is the amidase domain of bifunctional Escherichia coli glutathionylspermidine synthetase/amidase, and it catalyses the hydrolysis of Gsp (glutathionylspermidine) into glutathione and spermidine [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Bifunctional glutathionylspermidine synthetase/amidase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding glutathionylspermidine amidase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds acid-ammonia (or amide) ligase activity glutathionylspermidine synthase activity ligase activity, forming carbon-nitrogen bonds ligase activity cation binding metal ion binding	spermidine metabolic process amine metabolic process metabolic process cellular process polyamine metabolic process biogenic amine metabolic process glutathione metabolic process modified amino acid metabolic process sulfur compound metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B	IPR007921	CHAP domain	Domain
A, B	IPR051705	Glutathionylspermidine Synthetase/Amidase	Family
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR005494	Glutathionylspermidine synthase, pre-ATP-grasp-like domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.