1UC8 | pdb_00001uc8

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)
B	d1uc8b1	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	d1uc8b2	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)
A	d1uc8a1	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	d1uc8a2	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)
B	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)
A	SCOP2B Superfamily	PreATP-grasp domain	8041709	3001680	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8041710	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	Hexapep,Acetyltransf_11	e1uc8B1	A: alpha arrays	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Hexapep,Acetyltransf_11	ECOD (v295.2)
B	Ras	e1uc8B2	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: Ras	ECOD (v295.2)
A	RimK	e1uc8A1	A: beta duplicates or obligate multimers	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (v295.2)
A	LysX_preATP_grasp	e1uc8A2	A: alpha arrays	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: LysX_preATP_grasp	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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	lysine biosynthesis enzyme	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	small molecule biosynthetic process oxoacid metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule biosynthetic process oxoacid metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule metabolic process cellular response to stimulus SOS response cellular response to stress response to stimulus DNA damage response response to stress	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