3EN9 | pdb_00003en9

Structure of the Methanococcus jannaschii KAE1-BUD32 fusion protein

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	YgjD/Kae1-like	8058155	4000383	SCOP2 (2022-06-29)
A	SCOP2 Family	RIO1-like kinases	8058157	4000233	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8092403	3000092	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Protein kinase-like (PK-like)	8058158	3000066	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8058156	3000092	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8058158	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8092403	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8058156	3000092	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	RIO1	e3en9A1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: RIO1	ECOD (1.6)
A	Peptidase_M22_C_1	e3en9A4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Peptidase_M22_C_1	ECOD (1.6)
A	Peptidase_M22_N	e3en9A5	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Peptidase_M22_N	ECOD (1.6)
B	RIO1	e3en9B2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: RIO1	ECOD (1.6)
B	Peptidase_M22_C_1	e3en9B3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Peptidase_M22_C_1	ECOD (1.6)
B	Peptidase_M22_N	e3en9B4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Peptidase_M22_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00814	tRNA N6-adenosine threonylcarbamoyltransferase (TsaD)	tRNA N6-adenosine threonylcarbamoyltransferase	-	Family
A, B	PF01163	RIO domain (RIO1)	RIO domain	This is the atypical serine kinase domain found in RIO family of proteins and related sequences, which is conserved in archaea, bacteria and eukaryotes [5,6]. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, ...	This is the atypical serine kinase domain found in RIO family of proteins and related sequences, which is conserved in archaea, bacteria and eukaryotes [5,6]. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined [4]. This domain is also found at the C-terminal of EKC/KEOPS complex subunit BUD32 from Fungi and Kae1/Bud32 from archaea [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	O-sialoglycoprotein endopeptidase/protein kinase	protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity histone H3S57 kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H3 kinase activity histone modifying activity catalytic activity histone kinase activity histone H2AS121 kinase activity histone H2A kinase activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity histone H3S57 kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H3 kinase activity histone modifying activity catalytic activity histone kinase activity histone H2AS121 kinase activity histone H2A kinase activity protein serine/threonine/tyrosine kinase activity Rho-dependent protein serine/threonine kinase activity AMP-activated protein kinase activity peptidase activity metalloendopeptidase activity hydrolase activity metallopeptidase activity endopeptidase activity histone H2AT120 kinase activity DNA-dependent protein kinase activity histone H3T45 kinase activity histone H2AXS139 kinase activity histone H2AX kinase activity histone H4S1 kinase activity histone H4 kinase activity acyltransferase activity N(6)-L-threonylcarbamoyladenine synthase activity acyltransferase activity, transferring groups other than amino-acyl groups protein serine kinase activity 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 transition metal ion binding iron ion binding metal ion binding histone H3T11 kinase activity histone H3S28 kinase activity histone H3T6 kinase activity 3-phosphoinositide-dependent protein kinase activity histone H2B kinase activity histone H2BS36 kinase activity histone H3T3 kinase activity zinc ion binding histone H2AS1 kinase activity ribosomal protein S6 kinase activity histone H3S10 kinase activity histone H2BS14 kinase activity	tRNA threonylcarbamoyladenosine modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA threonylcarbamoyladenosine modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA threonylcarbamoyladenosine metabolic process metabolic process cellular process macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex catalytic complex transferase complex EKC/KEOPS complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR022495	Serine/threonine-protein kinase Bud32	Family
A, B	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B	IPR009220	Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein	Family
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR017860	Peptidase M22, conserved site	Conserved Site
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR000905	Gcp-like domain	Domain
A, B	IPR034680	tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaeal/eukaryotic	Family
A, B	IPR017861	Kae1/TsaD family	Family
A, B	IPR018934	RIO-type 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.