5ZCT | pdb_00005zct

The crystal structure of the poly-alpha-L-glutamate peptides synthetase RimK at 2.05 angstrom resolution.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RimK	e5zctA1	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	PRK10446	e5zctA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PRK10446	ECOD (1.6)
B	RimK	e5zctB2	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	PRK10446	e5zctB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PRK10446	ECOD (1.6)
C	RimK	e5zctC1	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)
C	PRK10446	e5zctC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PRK10446	ECOD (1.6)
G	RimK	e5zctG2	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)
G	PRK10446	e5zctG1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PRK10446	ECOD (1.6)
H	RimK	e5zctH2	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)
H	PRK10446	e5zctH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PRK10446	ECOD (1.6)
F	RimK	e5zctF1	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)
F	PRK10446	e5zctF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PRK10446	ECOD (1.6)
E	RimK	e5zctE2	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)
E	PRK10446	e5zctE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PRK10446	ECOD (1.6)
D	RimK	e5zctD1	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)
D	PRK10446	e5zctD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PRK10446	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 (utative)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (utative)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (utative)
C	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
C	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
C	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (utative)
G	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
G	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
G	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (utative)
H	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
H	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
H	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (utative)
F	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
F	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
F	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (utative)
E	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
E	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
E	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (utative)
D	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
D	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
D	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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, C, D, E A, B, C, D, E, F, G, H	PF18030	RimK PreATP-grasp domain (Rimk_N)	RimK PreATP-grasp domain	This is the N-terminal domain found in Escherichia coli RimK proteins (Ribosomal protein S6-L-glutamate ligase). This domain precedes the ATP-grasp domain Pfam:PF08443 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Ribosomal protein S6--L-glutamate ligase	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 identical protein binding protein binding	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 biosynthetic 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 biosynthetic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011761	ATP-grasp fold	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR041107	RimK, preATP-grasp domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023533	Ribosomal protein bS6-L-glutamate ligase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004666	Ribosomal bS6 modification enzyme RimK/Lysine biosynthesis enzyme LysX	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013651	ATP-grasp fold, RimK-type	Domain

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The crystal structure of the poly-alpha-L-glutamate peptides synthetase RimK at 2.05 angstrom resolution.

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

5ZCT | pdb_00005zct