8W4J | pdb_00008w4j

Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I

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)
F	SCOP2B Superfamily	MtdA-like	8056062	3000046	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	MtdA-like	8056062	3000046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8056062	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8056062	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8056062	3000046	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MtdA-like	8056062	3000046	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth I], H [auth J]	PF13415	FBX42, beta-propeller domain (Beta-prop_FBX42)	FBX42, beta-propeller domain	-	Repeat
G [auth I], H [auth J]	PF07707	BTB And C-terminal Kelch (BACK)	BTB And C-terminal Kelch	This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD, ...	This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD, personal observation).	Domain
G [auth I], H [auth J]	PF00651	BTB/POZ domain (BTB)	BTB/POZ domain	The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family o ...	The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation [2]. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule [3]. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [4,5,6]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.	Domain
G [auth I], H [auth J]	PF01344	Kelch motif (Kelch_1)	Kelch motif	-	Repeat
G [auth I], H [auth J]	PF13964	Calicin, beta-propeller domain (Beta-prop_Calicin)	Calicin, beta-propeller domain	-	Repeat
A, B, C, D, E A, B, C, D, E, F	PF02812	Glu/Leu/Phe/Val dehydrogenase, dimerisation domain (ELFV_dehydrog_N)	Glu/Leu/Phe/Val dehydrogenase, dimerisation domain		Domain
A, B, C, D, E A, B, C, D, E, F	PF00208	Glutamate/Leucine/Phenylalanine/Valine dehydrogenase (ELFV_dehydrog)	Glutamate/Leucine/Phenylalanine/Valine dehydrogenase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth I], H [auth J]	Kelch-like protein 22	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding 14-3-3 protein binding	regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process multicellular organismal process negative regulation of biological process negative regulation of type I interferon production cytokine production negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process type I interferon production negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production cell division cellular response to stimulus regulation of cell cycle phase transition response to stimulus spindle checkpoint signaling negative regulation of cell cycle regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling signal transduction cell cycle mitotic sister chromatid separation chromosome segregation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling negative regulation of cellular component organization regulation of cell cycle process sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition regulation of mitotic sister chromatid segregation mitotic cell cycle process regulation of chromosome separation negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of mitotic sister chromatid separation regulation of metaphase/anaphase transition of cell cycle signaling spindle assembly checkpoint signaling cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle regulation of mitotic cell cycle mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition regulation of cell cycle negative regulation of chromosome separation cell cycle process mitotic nuclear division negative regulation of mitotic cell cycle phase transition organelle fission chromosome organization negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling organelle organization nuclear division negative regulation of chromosome segregation negative regulation of nuclear division negative regulation of organelle organization chromosome separation regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition catabolic process proteolysis involved in protein catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein metabolic process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of TORC1 signaling positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling positive regulation of signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity regulation of response to biotic stimulus positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains immune response to tumor cell positive regulation of lymphocyte mediated immunity regulation of response to tumor cell response to biotic stimulus T cell mediated immune response to tumor cell regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of T cell mediated immune response to tumor cell positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune effector process positive regulation of adaptive immune response positive regulation of immune system process regulation of T cell mediated immunity response to tumor cell positive regulation of immune response to tumor cell immune response regulation of adaptive immune response regulation of immune response to tumor cell adaptive immune response immune effector process positive regulation of T cell mediated immune response to tumor cell regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity immune system process positive regulation of T cell mediated immunity regulation of immune response positive regulation of response to tumor cell cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid negative regulation of catabolic process autophagy regulation of catabolic process regulation of autophagy negative regulation of autophagy process utilizing autophagic mechanism protein monoubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to L-leucine cellular response to oxygen-containing compound response to L-leucine regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of cell-cell adhesion positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton polymeric cytoskeletal fiber spindle spindle microtubule polar microtubule intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton polymeric cytoskeletal fiber spindle spindle microtubule polar microtubule spindle pole supramolecular fiber microtubule supramolecular polymer supramolecular complex cytoplasm cytosol membrane-bounded organelle intracellular membrane-bounded organelle mitotic spindle lytic vacuole vacuole lysosome intercellular bridge cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex Cul3-RING ubiquitin ligase complex intracellular protein-containing complex nucleus
A, B, C, D, E A, B, C, D, E, F	Glutamate dehydrogenase 1, mitochondrial	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity glutamate dehydrogenase [NAD(P)+] activity oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor catalytic activity glutamate dehydrogenase (NADP+) activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity glutamate dehydrogenase [NAD(P)+] activity oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor catalytic activity glutamate dehydrogenase (NADP+) activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding organic acid binding L-leucine binding amino acid binding carboxylic acid binding adenyl ribonucleotide binding adenyl nucleotide binding ATP binding NAD+ binding NAD binding ADP binding identical protein binding protein binding protein homodimerization activity protein dimerization activity glutamate dehydrogenase (NAD+) activity	tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process catabolic process amino acid metabolic process organic acid catabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process carboxylic acid catabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process catabolic process amino acid metabolic process organic acid catabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process carboxylic acid catabolic process glutamate metabolic process amino acid catabolic process L-glutamate catabolic process dicarboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process developmental process multicellular organismal process head development animal organ development brain development nervous system development substantia nigra development multicellular organism development central nervous system development midbrain development anatomical structure development neural nucleus development system development glutamine metabolic process positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport regulation of cellular process positive regulation of establishment of protein localization cell communication localization positive regulation of insulin secretion intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of biological process regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion positive regulation of protein localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport signaling positive regulation of biological process positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of cellular process positive regulation of peptide secretion regulation of signaling regulation of transport secretion regulation of peptide transport biological regulation regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion positive regulation of signaling glutamine family amino acid biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process dicarboxylic acid biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process glutamate biosynthetic process alpha-amino acid biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth I], H [auth J]	IPR000210	BTB/POZ domain	Domain
G [auth I], H [auth J]	IPR006652	Kelch repeat type 1	Repeat
G [auth I], H [auth J]	IPR011705	BTB/Kelch-associated	Domain
G [auth I], H [auth J]	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
G [auth I], H [auth J]	IPR017096	BTB-kelch protein	Family
G [auth I], H [auth J]	IPR030575	Kelch-like protein 22, BACK domain	Domain
G [auth I], H [auth J]	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006097	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR033922	NAD(P) binding domain of glutamate dehydrogenase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR006095	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR006096	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR033524	Leu/Phe/Val dehydrogenases active site	Active Site
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G [auth I], H [auth J]	Pharos: Q53GT1	large cell medulloblastoma malignant mesothelioma psoriasis
A, B, C, D, E A, B, C, D, E, F	Pharos: P00367	hyperinsulinism-hyperammonemia syndrome hyperinsulinism Hyperammonemia hyperinsulinemic hypoglycemia osteosarcoma plasma cell myeloma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor fetal growth restriction gout intellectual disability medulloblastoma ovarian cancer primitive neuroectodermal tumor large cell medulloblastoma hyperinsulinism-hyperammonemia syndrome hyperinsulinism Hyperammonemia hyperinsulinemic hypoglycemia osteosarcoma plasma cell myeloma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor fetal growth restriction gout intellectual disability medulloblastoma ovarian cancer primitive neuroectodermal tumor large cell medulloblastoma pancreatic ductal adenocarcinoma psoriasis Down syndrome glioblastoma inborn errors of metabolism malignant glioma

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.