Annotations: 9DPD

Cryo-EM structure of SerRS dimer in complex with one SIRT2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8034236	3001728	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth D]	PF02403	Seryl-tRNA synthetase N-terminal domain (Seryl_tRNA_N)	Seryl-tRNA synthetase N-terminal domain	This domain is found associated with the Pfam tRNA synthetase class II domain (Pfam:PF00587) and represents the N-terminal domain of seryl-tRNA synthetase.	Domain
C	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth D]	Serine--tRNA ligase, cytoplasmic	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding tRNA binding adenyl ribonucleotide binding DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding tRNA 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 ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity selenocysteine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity serine-tRNA ligase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity molecular adaptor activity enzyme binding	multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of vascular endothelial growth factor production negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of vascular endothelial growth factor production negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression vascular endothelial growth factor production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process tRNA modification RNA metabolic process primary metabolic process 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 RNA processing translation protein biosynthetic process cytoplasmic translation protein metabolic process selenocysteine incorporation regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of protein metabolic process translational readthrough regulation of translation translational elongation amino acid activation tRNA aminoacylation amino acid metabolic process tRNA aminoacylation for protein translation seryl-tRNA aminoacylation regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II regulation of DNA-templated transcription negative regulation of RNA metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus intracellular membrane-bounded organelle
C	NAD-dependent protein deacetylase sirtuin-2	histone deacetylase binding protein binding binding enzyme binding NAD-dependent protein demyristoylase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity histone methacryllysine demethacrylase activity catalytic activity, acting on a protein histone modifying activity deacetylase activity tubulin deacetylase activity histone deacetylase binding protein binding binding enzyme binding NAD-dependent protein demyristoylase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity histone methacryllysine demethacrylase activity catalytic activity, acting on a protein histone modifying activity deacetylase activity tubulin deacetylase activity protein lysine deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides deacylase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity ubiquitin binding ubiquitin-like protein binding histone acetyltransferase binding transcription factor binding DNA-binding transcription factor binding NAD-dependent protein depalmitoylase activity histone deacetylase activity, NAD-dependent histone H4K16 deacetylase activity, NAD-dependent NAD-dependent protein lysine deacylase activity histone H4K deacetylase activity NAD-dependent protein lysine deacetylase activity histone benzoyllysine debenzoylase activity NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding pentosyltransferase activity NAD+ poly-ADP-ribosyltransferase activity glycosyltransferase activity chromatin binding cation binding transition metal ion binding zinc ion binding metal ion binding	multicellular organismal process oligodendrocyte progenitor proliferation regulation of cellular process negative regulation of neural precursor cell proliferation cellular developmental process regulation of developmental process negative regulation of biological process cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis regulation of cell development regulation of nervous system development neurogenesis multicellular organism development multicellular organismal process oligodendrocyte progenitor proliferation regulation of cellular process negative regulation of neural precursor cell proliferation cellular developmental process regulation of developmental process negative regulation of biological process cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis regulation of cell development regulation of nervous system development neurogenesis multicellular organism development negative regulation of neurogenesis gliogenesis cell differentiation anatomical structure development negative regulation of cellular process regulation of multicellular organismal process negative regulation of nervous system development negative regulation of cell differentiation negative regulation of oligodendrocyte progenitor proliferation system development regulation of neural precursor cell proliferation developmental process regulation of multicellular organismal development regulation of biological process negative regulation of cell population proliferation cell population proliferation negative regulation of developmental process biological regulation nervous system development negative regulation of gliogenesis negative regulation of cell development regulation of cell population proliferation cellular process neural precursor cell proliferation negative regulation of multicellular organismal process regulation of oligodendrocyte progenitor proliferation cell division peripheral nervous system axon ensheathment peripheral nervous system development glial cell development myelination Schwann cell development axon ensheathment ensheathment of neurons glial cell differentiation myelination in peripheral nervous system Schwann cell differentiation cellular response to stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway response to stimulus regulation of NLRP3 inflammasome complex assembly regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly regulation of immune system process signal transduction negative regulation of NLRP3 inflammasome complex assembly positive regulation of immune system process innate immune response-activating signaling pathway negative regulation of cellular component organization immune response response to other organism regulation of innate immune response response to external stimulus regulation of inflammasome-mediated signaling pathway negative regulation of protein-containing complex assembly regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly positive regulation of defense response activation of innate immune response regulation of immune response inflammatory response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular component organization regulation of response to external stimulus intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus cellular component organization regulation of protein-containing complex assembly positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response protein-containing complex assembly response to external biotic stimulus cellular component organization or biogenesis regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus protein-containing complex organization defense response to symbiont regulation of cellular component biogenesis negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication negative regulation of inflammasome-mediated signaling pathway response to redox state catabolic process autophagy metabolic process process utilizing autophagic mechanism positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process response to oxidative stress cellular response to chemical stimulus cellular response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress negative regulation of metabolic process reactive oxygen species metabolic process negative regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process negative regulation of catabolic process regulation of autophagy negative regulation of autophagy RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process fat cell differentiation negative regulation of fat cell differentiation regulation of fat cell differentiation mitotic nuclear membrane reassembly membrane biogenesis mitotic cell cycle nuclear membrane reassembly cell cycle endomembrane system organization cell cycle process membrane organization mitotic nuclear division organelle fission nuclear membrane organization membrane assembly nuclear division organelle organization nucleus organization mitotic cell cycle process mitotic nuclear membrane organization nuclear envelope organization response to epinephrine cellular response to epinephrine stimulus lipid catabolic process lipid metabolic process head development animal organ development brain development substantia nigra development central nervous system development midbrain development neural nucleus development regulation of muscle tissue development regulation of striated muscle tissue development tissue development negative regulation of muscle tissue development striated muscle tissue development muscle structure development negative regulation of muscle organ development regulation of muscle organ development muscle tissue development muscle organ development negative regulation of striated muscle tissue development chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression negative regulation of gene expression, epigenetic positive regulation of oocyte maturation sexual reproduction regulation of reproductive process reproductive process regulation of oocyte maturation cellular process involved in reproduction in multicellular organism positive regulation of cell maturation developmental process involved in reproduction female gamete generation gamete generation oocyte development positive regulation of developmental process positive regulation of cell differentiation cell maturation regulation of cell maturation positive regulation of reproductive process multicellular organismal reproductive process oogenesis positive regulation of cell development developmental maturation anatomical structure maturation germ cell development oocyte maturation oocyte differentiation positive regulation of organelle organization positive regulation of cellular component organization meiotic cell cycle process positive regulation of cell cycle process meiotic nuclear division regulation of cell cycle regulation of meiotic cell cycle regulation of cell cycle process meiotic cell cycle positive regulation of nuclear division positive regulation of meiotic cell cycle regulation of organelle organization positive regulation of cell cycle regulation of meiotic nuclear division regulation of nuclear division positive regulation of meiotic nuclear division regulation of chromosome segregation metaphase chromosome alignment localization chromosome localization organelle localization regulation of attachment of spindle microtubules to kinetochore chromosome segregation positive regulation of chromosome segregation attachment of spindle microtubules to kinetochore positive regulation of attachment of spindle microtubules to kinetochore nuclear chromosome segregation regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding positive regulation of binding positive regulation of DNA binding phosphorylation phosphate-containing compound metabolic process regulation of phosphorylation regulation of phosphorus metabolic process phosphorus metabolic process skeletal muscle cell differentiation skeletal muscle tissue development skeletal muscle organ development regulation of skeletal muscle cell differentiation negative regulation of skeletal muscle cell differentiation negative regulation of satellite cell differentiation skeletal muscle satellite cell differentiation peptidyl-lysine deacetylation peptidyl-lysine modification macromolecule deacylation protein deacetylation protein deacylation macromolecule modification peptidyl-amino acid modification protein modification process regulation of cell cycle phase transition cell cycle phase transition exit from mitosis regulation of mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of exit from mitosis mitotic cell cycle phase transition response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process positive regulation of fatty acid biosynthetic process regulation of small molecule metabolic process positive regulation of biosynthetic process positive regulation of lipid metabolic process small molecule metabolic process positive regulation of fatty acid metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process positive regulation of lipid biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process monocarboxylic acid metabolic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process positive regulation of cell division regulation of cell division positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process regulation of execution phase of apoptosis positive regulation of execution phase of apoptosis execution phase of apoptosis apoptotic process programmed cell death subtelomeric heterochromatin formation constitutive heterochromatin formation response to nutrient levels cellular response to caloric restriction response to caloric restriction negative regulation of protein catabolic process negative regulation of protein metabolic process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of myelination regulation of protein modification process regulation of protein phosphorylation regulation of peptidyl-threonine phosphorylation negative regulation of phosphate metabolic process negative regulation of protein modification process peptidyl-threonine modification protein phosphorylation negative regulation of protein phosphorylation negative regulation of peptidyl-threonine phosphorylation negative regulation of phosphorus metabolic process negative regulation of phosphorylation peptidyl-threonine phosphorylation tubulin deacetylation nucleolar chromatin organization rDNA heterochromatin formation nucleolus organization facultative heterochromatin formation	axon cell projection cellular anatomical structure main axon juxtaparanode region of axon neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body perikaryon neuronal cell body cell-cell junction anchoring junction cell junction axon cell projection cellular anatomical structure main axon juxtaparanode region of axon neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body perikaryon neuronal cell body cell-cell junction anchoring junction cell junction paranodal junction intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome midbody membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen microtubule organizing center cytoskeleton centriole microtubule cytoskeleton cell periphery plasma membrane membrane protein-containing complex chromatin silencing complex nuclear protein-containing complex lateral loop myelin sheath chromatin heterochromatin perinuclear region of cytoplasm spindle chromosome, telomeric region chromosomal region polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex mitochondrion paranode region of axon centrosome glial cell projection mitotic spindle growth cone distal axon site of polarized growth compact myelin Schmidt-Lanterman incisure meiotic spindle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth D]	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A [auth B], B [auth D]	IPR002317	Serine-tRNA ligase, type1	Family
A [auth B], B [auth D]	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A [auth B], B [auth D]	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A [auth B], B [auth D]	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Homologous Superfamily
A [auth B], B [auth D]	IPR033729	Serine-tRNA ligase catalytic core domain	Domain
A [auth B], B [auth D]	IPR042103	Serine-tRNA synthetase, type1, N-terminal domain superfamily	Homologous Superfamily
A [auth B], B [auth D]	IPR015866	Serine-tRNA synthetase, type1, N-terminal	Domain
C	IPR003000	Sirtuin family	Family
C	IPR017328	Sirtuin, class I	Family
C	IPR026590	Sirtuin family, catalytic core domain	Domain
C	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
C	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
C	IPR050134	NAD-dependent sirtuin protein deacylases	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], B [auth D]	: P49591	neurodevelopmental disorder with microcephaly, ataxia, and seizures abdominal aortic aneurysm malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm epilepsy myocardial infarction pancreatic ductal adenocarcinoma peripheral arterial disease heart disease pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma
C	: Q8IXJ6	neurodegenerative disease adrenal cortex carcinoma large cell medulloblastoma Disturbance in mood medulloblastoma osteosarcoma

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.