1UC9

Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8

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	d1uc9a1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Lysine biosynthesis enzyme LysX, N-terminal domain	Lysine biosynthesis enzyme LysX, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1uc9a2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Lysine biosynthesis enzyme LysX ATP-binding domain	Lysine biosynthesis enzyme LysX ATP-binding domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1uc9b1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Lysine biosynthesis enzyme LysX, N-terminal domain	Lysine biosynthesis enzyme LysX, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1uc9b2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Lysine biosynthesis enzyme LysX ATP-binding domain	Lysine biosynthesis enzyme LysX ATP-binding domain	(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	SCOP2 Family	Lysine biosynthesis enzyme LysX ATP-binding domain	8029331	4001590	SCOP2 (2022-06-29)
A	SCOP2 Family	Lysine biosynthesis enzyme LysX N-terminal domain	8029330	4001028	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glutathione synthetase ATP-binding domain-like	8041710	3000094	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PreATP-grasp domain	8041709	3001680	SCOP2 (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	e1uc9A1	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	e1uc9A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: LysX_arch	ECOD (1.6)
B	RimK	e1uc9B1	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	e1uc9B2	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	lysine biosynthesis enzyme	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity ligase activity cation binding metal ion binding	lysine metabolic process lysine biosynthetic process via aminoadipic acid oxoacid metabolic process cellular biosynthetic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic 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 organic substance metabolic process organic substance biosynthetic process lysine metabolic process lysine biosynthetic process via aminoadipic acid oxoacid metabolic process cellular biosynthetic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic 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 organic substance metabolic process organic substance biosynthetic process small molecule metabolic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process macromolecule modification protein metabolic process macromolecule metabolic process protein modification process	-

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	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B	IPR004666	Ribosomal bS6 modification enzyme RimK/Lysine biosynthesis enzyme LysX	Family
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR013651	ATP-grasp fold, RimK-type	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.