3ERR | pdb_00003err

Microtubule binding domain from mouse cytoplasmic dynein as a fusion with seryl-tRNA synthetase

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	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	8101644	4001782	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II aaRS and biotin synthetases	8101645	3000058	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8101645	3000058	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	zf-CCCH_4	e3errA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (v294.1)
A	LYTB	e3errA3	A: a/b three-layered sandwiches	X: cradle loop barrel	H: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase	T: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase	F: LYTB	ECOD (v294.1)
B		e3errB3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.920.60	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	1.20.920.60	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00587	tRNA synthetase class II core domain (G, H, P, S and T) (tRNA-synt_2b)	tRNA synthetase class II core domain (G, H, P, S and T)	tRNA-synt_2b is a family of largely threonyl-tRNA members.	Domain
A, B	PF12777	Microtubule-binding stalk of dynein motor (MT)	Microtubule-binding stalk of dynein motor	the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures describ ...	the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA synthetase from Thermus thermophilus	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 ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA serine-tRNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity dynein light intermediate chain binding protein binding microtubule motor activity polypeptide conformation or assembly isomerase activity isomerase activity cytoskeletal motor activity minus-end-directed microtubule motor activity macromolecular conformation isomerase activity ATP-dependent activity dynein intermediate chain binding identical protein binding	oxoacid metabolic process modified amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process modified amino acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process oxoacid metabolic process modified amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process modified amino acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process selenocysteine metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process L-selenocysteine biosynthetic process alpha-amino acid biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process seryl-tRNA aminoacylation macromolecule metabolic process protein metabolic process cell division establishment of organelle localization cellular localization transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly membraneless organelle assembly cellular component organization or biogenesis microtubule-based movement microtubule-based process cilium movement stress granule assembly microtubule cytoskeleton organization spindle localization establishment of spindle localization cell cycle cytoskeleton organization cell cycle process regulation of localization regulation of biological process biological regulation metaphase chromosome alignment chromosome localization nuclear chromosome segregation regulation of metaphase plate congression chromosome segregation positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process positive regulation of spindle assembly positive regulation of cell cycle process regulation of cell cycle positive regulation of cellular process spindle organization regulation of cell cycle process positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of microtubule-based process regulation of spindle organization regulation of cellular component biogenesis spindle assembly regulation of organelle organization positive regulation of cell cycle regulation of spindle assembly regulation of organelle assembly regulation of microtubule cytoskeleton organization positive regulation of organelle assembly regulation of mitotic spindle organization mitotic cell cycle microtubule cytoskeleton organization involved in mitosis mitotic spindle organization mitotic cell cycle process cytoplasmic microtubule organization supramolecular fiber organization multicellular organismal process homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process regulation of transport positive regulation of transport regulation of cellular localization positive regulation of intracellular transport regulation of intracellular transport retrograde axonal transport axonal transport axo-dendritic transport microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle envelope organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system somatodendritic compartment cell body neuronal cell body cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle envelope organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system somatodendritic compartment cell body neuronal cell body axon cell projection neuron projection plasma membrane bounded cell projection protein-containing complex cytoplasmic dynein complex catalytic complex dynein complex intracellular membraneless organelle cytoskeleton membraneless organelle microtubule associated complex microtubule cytoskeleton actin-based cell projection filopodium polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex neuron projection cytoplasm axon cytoplasm cell periphery cell cortex centrosome microtubule organizing center manchette cytoplasmic microtubule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR042103	Serine-tRNA synthetase, type1, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR002317	Serine-tRNA ligase, type1	Family
A, B	IPR015866	Serine-tRNA synthetase, type1, N-terminal	Domain
A, B	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A, B	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Homologous Superfamily
A, B	IPR033729	Serine-tRNA ligase catalytic core domain	Domain
A, B	IPR026983	Dynein heavy chain	Family
A, B	IPR013602	Dynein heavy chain, linker	Domain
A, B	IPR041658	Dynein heavy chain, AAA lid domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR042222	Dynein heavy chain, domain 2, N-terminal	Homologous Superfamily
A, B	IPR043160	Dynein heavy chain, C-terminal domain, barrel region	Homologous Superfamily
A, B	IPR042219	Dynein heavy chain, AAA lid domain superfamily	Homologous Superfamily
A, B	IPR035706	Dynein heavy chain, ATP-binding dynein motor region	Domain
A, B	IPR041228	Dynein heavy chain, C-terminal domain	Domain
A, B	IPR054354	Dynein 2 heavy chain 1, cytoplasmic, ATPase lid domain	Domain
A, B	IPR003593	AAA+ ATPase domain	Domain
A, B	IPR041466	Dynein heavy chain, AAA 5 extension domain	Domain
A, B	IPR042228	Dynein heavy chain, linker, subdomain 3	Homologous Superfamily
A, B	IPR035699	Dynein heavy chain, hydrolytic ATP-binding dynein motor region	Domain
A, B	IPR024743	Dynein heavy chain, coiled coil stalk	Domain
A, B	IPR013594	Dynein heavy chain, tail	Domain
A, B	IPR043157	Dynein heavy chain, AAA1 domain, small subdomain	Homologous Superfamily
A, B	IPR004273	Dynein heavy chain, D6 P-loop domain	Domain
A, B	IPR024317	Dynein heavy chain, AAA module D4	Domain