3VPD | pdb_00003vpd

LysX from Thermus thermophilus complexed with AMP-PNP

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)
A	d3vpda1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	automated matches	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d3vpda2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Lysine biosynthesis enzyme LysX ATP-binding domain	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d3vpdb1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	automated matches	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d3vpdb2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Lysine biosynthesis enzyme LysX ATP-binding domain	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8041710	3000094	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PreATP-grasp domain	8041709	3001680	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8041710	3000094	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8041709	3001680	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)
A	RimK	e3vpdA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
A	LysX_arch	e3vpdA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: LysX_arch	ECOD (1.6)
B	RimK	e3vpdB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
B	LysX_arch	e3vpdB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: LysX_arch	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08443	RimK-like ATP-grasp domain (RimK)	RimK-like ATP-grasp domain	This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK [1].	Domain
A, B	PF22626	LysX preATP-grasp domain (LysX_preATP_grasp)	LysX preATP-grasp domain	This entry represents the preATP-grasp domain found at the N-terminal of archaeal LysX, ArgX and similar proteins. LysX catalyses the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxy ...	This entry represents the preATP-grasp domain found at the N-terminal of archaeal LysX, ArgX and similar proteins. LysX catalyses the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW [1,2]. ArgX catalyses the ATP-dependent formation of a covalent bond between the amino group of glutamate and the gamma-carboxyl group of the C-terminal glutamate residue in LysW [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ribosomal protein S6 modification protein	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 cation binding metal ion binding ribosomal S6-glutamic acid ligase activity acid-amino acid ligase activity catalytic activity, acting on a protein protein-glutamic acid ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular response to stimulus SOS response cellular response to stress response to stimulus DNA damage response response to stress lysine metabolic process macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular response to stimulus SOS response cellular response to stress response to stimulus DNA damage response response to stress lysine metabolic process lysine biosynthetic process via aminoadipic acid oxoacid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011761	ATP-grasp fold	Domain
A, B	IPR011870	Lysine biosynthesis enzyme LysX	Family
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B	IPR004666	Ribosomal bS6 modification enzyme RimK/Lysine biosynthesis enzyme LysX	Family
A, B	IPR054562	LysX/ArgX, preATP-grasp domain	Domain
A, B	IPR013651	ATP-grasp fold, RimK-type	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.