8PU0 | pdb_00008pu0

Cryo-EM structure of human Elp123 in complex with tRNA, desulpho-CoA, 5'-deoxyadenosine and methionine

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth E]	PF23797	ELP1 N-terminal second beta-propeller (Beta-prop_ELP1_2nd)	ELP1 N-terminal second beta-propeller	-	Repeat
A, D [auth E]	PF23936	ELP1 three-helix bundle (HB_ELP1)	ELP1 three-helix bundle	This entry represents the helical bundle domain found within the C-terminal dimerization domain of Elongator complex protein 1 (ELP1), from eukaryotes. Elongator is a conserved protein complex implicated in multiple processes including regulation of ...	This entry represents the helical bundle domain found within the C-terminal dimerization domain of Elongator complex protein 1 (ELP1), from eukaryotes. Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia [1]. The C-terminal dimerization domain consists of 28 alpha-helices organised in three domains: an elongated alpha-solenoid domain (helices 1 to 14); a TPR domain, formed by six double-helix repeats (helices 15 to 26); and a three-helix bundle, C-terminal cap (helices 26 to 28) [2]. ELP1 self-association contributes to its stability and is important for Elongator assembly [2]. ELP1 is considered to function both as a scaffold, for Elongator complex ELP2 and ELP3 binding, and as a docking site for various factors that regulate Elongator activity [2-4]. Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling [5].	Domain
A, D [auth E]	PF23925	ELP1 alpha-solenoid (A-sol_ELP1)	ELP1 alpha-solenoid	-	Repeat
A, D [auth E]	PF04762	ELP1 first N-terminal beta-propeller (Beta-prop_ELP1_1st)	ELP1 first N-terminal beta-propeller	-	Repeat
A, D [auth E]	PF23878	ELP1 TPR domain (TPR_ELP1)	ELP1 TPR domain	-	Repeat
C	PF04055	Radical SAM superfamily (Radical_SAM)	Radical SAM superfamily	Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.	Domain
C	PF16199	Radical_SAM C-terminal domain (Radical_SAM_C)	Radical_SAM C-terminal domain	-	Family
C	PF23613	ELP3 N-terminal domain (ELP3_N)	ELP3 N-terminal domain	This domain is found N-terminal in the human Elongator complex protein 3 (ELP3) and related proteins. This protein is required for multiple modifications of tRNA. In the elongation complex, it acts as a tRNA uridine(34) acetyltransferase. It may also ...	This domain is found N-terminal in the human Elongator complex protein 3 (ELP3) and related proteins. This protein is required for multiple modifications of tRNA. In the elongation complex, it acts as a tRNA uridine(34) acetyltransferase. It may also act as a lysine acetyltransferase by mediating acetylation of target proteins [1]. The domain represented by this entry is predicted to fold into a globular structure consisting of two nearly orthogonal alpha-helical hairpins.	Domain
B	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth E]	Elongator complex protein 1	RNA binding binding tRNA binding nucleic acid binding	tRNA modification RNA metabolic process primary metabolic process tRNA wobble uridine modification 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 modification RNA metabolic process primary metabolic process tRNA wobble uridine modification 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 wobble base 5-methoxycarbonylmethyl-2-thiouridinylation tRNA wobble base modification metabolic process cellular process macromolecule metabolic process RNA processing regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process protein metabolic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex elongator holoenzyme complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C	Elongator complex protein 3	acetyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding RNA binding tRNA binding nucleic acid binding catalytic activity, acting on RNA acetyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding RNA binding tRNA binding nucleic acid binding catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA tRNA uridine(34) acetyltransferase activity cation binding ion binding metal ion binding	developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of metabolic process tRNA modification RNA metabolic process tRNA wobble uridine modification nucleobase-containing compound biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification tRNA processing macromolecule modification tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation tRNA wobble base modification RNA processing positive regulation of locomotion regulation of cell motility positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process neuron migration cellular developmental process generation of neurons neurogenesis cell differentiation DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol protein-containing complex catalytic complex elongator holoenzyme complex intracellular protein-containing complex
E [auth X]	tRNA Gln	-	-	-
B	Elongator complex protein 2	protein binding binding kinase binding enzyme binding protein kinase binding	cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT regulation of cell communication cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT regulation of cell communication cellular process signal transduction regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT tRNA modification RNA metabolic process primary metabolic process tRNA wobble uridine modification 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 wobble base modification metabolic process macromolecule metabolic process RNA processing transcription elongation by RNA polymerase II DNA-templated transcription DNA-templated transcription elongation transcription by RNA polymerase II regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process regulation of protein metabolic process translation protein biosynthetic process post-transcriptional regulation of gene expression regulation of translation protein metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol catalytic complex elongator holoenzyme complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth E]	IPR056167	ELP1, alpha-solenoid	Domain
A, D [auth E]	IPR006849	Elongator complex protein 1	Family
A, D [auth E]	IPR056169	ELP1, three-helical bundle	Domain
A, D [auth E]	IPR056166	ELP1, TPR domain	Domain
A, D [auth E]	IPR056165	ELP1, N-terminal second beta-propeller	Domain
A, D [auth E]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, D [auth E]	IPR056164	ELP1, first N-terminal beta-propeller	Domain
C	IPR007197	Radical SAM	Domain
C	IPR006638	Elp3/MiaA/NifB-like, radical SAM core domain	Domain
C	IPR000182	GNAT domain	Domain
C	IPR058240	Radical SAM superfamily	Homologous Superfamily
C	IPR034687	Elongator complex protein 3-like	Family
C	IPR032432	Radical SAM, C-terminal extension	Domain
C	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
C	IPR056591	ELP3-like, N-terminal domain	Domain
C	IPR039661	ELP3/YhcC	Family
B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B	IPR001680	WD40 repeat	Repeat
B	IPR037289	Elongator complex protein 2	Family
B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D [auth E]	Pharos: O95163	Riley-Day syndrome peripheral neuropathy breast carcinoma Neoplasm Invasiveness plasma cell myeloma attention deficit hyperactivity disorder, inattentive type Charcot-Marie-Tooth disease Hirschsprung disease, susceptibility to, 1 neurodegenerative disease breast cancer dermatomyositis large cell medulloblastoma osteosarcoma pancreatic ductal adenocarcinoma Pick disease Riley-Day syndrome peripheral neuropathy breast carcinoma Neoplasm Invasiveness plasma cell myeloma attention deficit hyperactivity disorder, inattentive type Charcot-Marie-Tooth disease Hirschsprung disease, susceptibility to, 1 neurodegenerative disease breast cancer dermatomyositis large cell medulloblastoma osteosarcoma pancreatic ductal adenocarcinoma Pick disease hereditary sensory and autonomic neuropathy ovarian cancer peripheral nervous system disease
C	Pharos: Q9H9T3	Neoplasm Invasiveness breast carcinoma amyotrophic lateral sclerosis osteosarcoma breast cancer gastric cancer ovarian cancer gastric carcinoma neurodegenerative disease vascular disease
B	Pharos: Q6IA86	intellectual disability intellectual disability, autosomal recessive 58 atypical teratoid rhabdoid tumor malignant glioma Mental Retardation, Psychosocial carcinoma of esophagus medulloblastoma osteosarcoma squamous cell carcinoma glioblastoma large cell medulloblastoma ovarian cancer