4K87 | pdb_00004k87

Crystal structure of human prolyl-tRNA synthetase (substrate bound form)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4k87A3	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: Phosphofructokinase N-terminal domain	T:	F:	ECOD (20:10:01)
A		e4k87A6	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
A	3.30.110.30	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	C-terminal domain of ProRS	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03129	Anticodon binding domain (HGTP_anticodon)	Anticodon binding domain	This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [1] it is probably the anticodon binding domain [2].	Domain
A	PF09180	Prolyl-tRNA synthetase, C-terminal (ProRS-C_1)	Prolyl-tRNA synthetase, C-terminal	Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-be ...	Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif [1].	Domain
A	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Proline--tRNA ligase	glutamate-tRNA ligase activity ligase activity, forming carbon-oxygen bonds aminoacyl-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 protein binding binding enzyme binding GTPase binding adenyl ribonucleotide binding nucleotide binding glutamate-tRNA ligase activity ligase activity, forming carbon-oxygen bonds aminoacyl-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 protein binding binding enzyme binding GTPase 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 identical protein binding protein homodimerization activity protein dimerization activity RNA binding RNA stem-loop binding nucleic acid binding proline-tRNA ligase activity cation binding transition metal ion binding zinc ion binding metal ion binding	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process import into cell regulation of localization transport regulation of lipid transport localization monocarboxylic acid transport fatty acid transport lipid import into cell long-chain fatty acid import into cell long-chain fatty acid transport organic anion transport carboxylic acid transport regulation of transport regulation of long-chain fatty acid import into cell lipid localization lipid transport establishment of localization regulation of fatty acid transport organic acid transport regulation of lipid localization macromolecule localization regulation of organic acid transport amino acid activation tRNA aminoacylation RNA metabolic process amino acid metabolic process tRNA aminoacylation for protein translation nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus response to peptide response to chemical immune system process defense response to other organism response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus glutamyl-tRNA aminoacylation prolyl-tRNA aminoacylation cellular response to stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to insulin cellular response to insulin stimulus cellular response to hormone stimulus	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex GAIT complex cell periphery plasma membrane membrane-bounded organelle cell projection sperm midpiece organelle cilium cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex GAIT complex cell periphery plasma membrane membrane-bounded organelle cell projection sperm midpiece organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection catalytic complex aminoacyl-tRNA synthetase multienzyme complex intracellular protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A	IPR009068	uS15/NS1, RNA-binding domain superfamily	Homologous Superfamily
A	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A	IPR004154	Anticodon-binding	Domain
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR053836	Nuclear-export cofactor Arc1-like, N-terminal domain	Domain
A	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
A	IPR004499	Proline-tRNA ligase, class IIa, archaeal-type	Family
A	IPR000738	WHEP-TRS domain	Domain
A	IPR004526	Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic	Family
A	IPR000924	Glutamyl/glutaminyl-tRNA synthetase	Family
A	IPR020058	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain	Domain
A	IPR017449	Prolyl-tRNA synthetase, class II	Homologous Superfamily
A	IPR020056	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, N-terminal	Homologous Superfamily
A	IPR049437	tRNA synthetases class I (E and Q), anti-codon binding domain	Domain
A	IPR020059	Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain	Domain
A	IPR011035	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, anti-codon-binding domain superfamily	Homologous Superfamily
A	IPR033721	Prolyl-tRNA synthetase, catalytic domain	Domain
A	IPR036282	Glutathione S-transferase, C-terminal domain superfamily	Homologous Superfamily
A	IPR016061	Proline-tRNA ligase, class II, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P07814	pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor astrocytic tumor Gaucher disease large cell medulloblastoma lung adenocarcinoma malignant glioma neurodegenerative disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis atypical teratoid rhabdoid tumor glioblastoma leukodystrophy lung cancer pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor astrocytic tumor Gaucher disease large cell medulloblastoma lung adenocarcinoma malignant glioma neurodegenerative disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis atypical teratoid rhabdoid tumor glioblastoma leukodystrophy lung cancer malignant pancreatic neoplasm non-small cell lung carcinoma ovarian cancer plasma cell myeloma breast cancer invasive ductal breast carcinoma leukodystrophy, hypomyelinating, 15 malignant ependymoma medulloblastoma oligodendroglioma