1NJ8 | pdb_00001nj8

Crystal Structure of Prolyl-tRNA Synthetase from Methanocaldococcus janaschii

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1nj8a1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	Prolyl-tRNA synthetase (ProRS) domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d1nj8a2	Alpha and beta proteins (a+b)	IF3-like	C-terminal domain of ProRS	C-terminal domain of ProRS	C-terminal domain of ProRS	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d1nj8a3	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Prolyl-tRNA synthetase (ProRS)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d1nj8a4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1nj8b1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	Prolyl-tRNA synthetase (ProRS) domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1nj8b2	Alpha and beta proteins (a+b)	IF3-like	C-terminal domain of ProRS	C-terminal domain of ProRS	C-terminal domain of ProRS	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1nj8b3	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Prolyl-tRNA synthetase (ProRS)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1nj8b4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1nj8c1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	Prolyl-tRNA synthetase (ProRS) domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1nj8c2	Alpha and beta proteins (a+b)	IF3-like	C-terminal domain of ProRS	C-terminal domain of ProRS	C-terminal domain of ProRS	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1nj8c3	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Prolyl-tRNA synthetase (ProRS)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1nj8c4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d1nj8d1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	Prolyl-tRNA synthetase (ProRS) domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d1nj8d2	Alpha and beta proteins (a+b)	IF3-like	C-terminal domain of ProRS	C-terminal domain of ProRS	C-terminal domain of ProRS	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d1nj8d3	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Prolyl-tRNA synthetase (ProRS)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d1nj8d4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	C-terminal domain of ProRS	8020983	4003809	SCOP2 (2022-06-29)
A	SCOP2 Family	Anticodon-binding domain of Class II aaRS	8020984	4000507	SCOP2 (2022-06-29)
A	SCOP2 Family	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	8020988	4001782	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C-terminal domain of ProRS	8033363	3001540	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II aaRS ABD-related	8033364	3000465	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II aaRS and biotin synthetases	8033368	3000058	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8033368	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS ABD-related	8033364	3000465	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-terminal domain of ProRS	8033363	3001540	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8033368	3000058	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II aaRS ABD-related	8033364	3000465	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	C-terminal domain of ProRS	8033363	3001540	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	C-terminal domain of ProRS	8033363	3001540	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Class II aaRS ABD-related	8033364	3000465	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8033368	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		e1nj8A1	A: IF3-like	X: C-terminal domain of ProRS	H: C-terminal domain of ProRS	T: ProRS-C_2	F:	ECOD (20:10:01)
A		e1nj8A3	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T:	F:	ECOD (20:10:01)
A		e1nj8A2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Pkinase	F:	ECOD (20:10:01)
B		e1nj8B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
B		e1nj8B2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Pkinase	F:	ECOD (20:10:01)
B		e1nj8B3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
C		e1nj8C1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
C		e1nj8C2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Pkinase	F:	ECOD (20:10:01)
C		e1nj8C3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
D		e1nj8D1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
D		e1nj8D2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Pkinase	F:	ECOD (20:10:01)
D		e1nj8D3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	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)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
B	3.30.110.30	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	C-terminal domain of ProRS	CATH (4.3.0)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
C	3.30.110.30	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	C-terminal domain of ProRS	CATH (4.3.0)
D	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
D	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
D	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, B, C, D	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, B, C, D	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, C, D	PF09181	Prolyl-tRNA synthetase, C-terminal (ProRS-C_2)	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Proline-tRNA Synthetase	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 catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity proline-tRNA ligase activity ligase activity	prolyl-tRNA aminoacylation amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid 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 biosynthetic process prolyl-tRNA aminoacylation amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid 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 biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B, C, D	IPR017449	Prolyl-tRNA synthetase, class II	Homologous Superfamily
A, B, C, D	IPR004154	Anticodon-binding	Domain
A, B, C, D	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B, C, D	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A, B, C, D	IPR033721	Prolyl-tRNA synthetase, catalytic domain	Domain
A, B, C, D	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR004499	Proline-tRNA ligase, class IIa, archaeal-type	Family
A, B, C, D	IPR002316	Proline-tRNA ligase, class IIa	Family
A, B, C, D	IPR015264	Prolyl-tRNA synthetase, class II, C-terminal, archaeal-type	Domain

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.